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Sample records for genome annotation expert

  1. IMG ER: A System for Microbial Genome Annotation Expert Review and Curation

    SciTech Connect

    Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.; Chu, Ken; Kyrpides, Nikos C.

    2009-05-25

    A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct. We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and efficient revision of microbial genome annotations. IMG ER provides tools for the review and curation of annotations of both new and publicly available microbial genomes within IMG's rich integrated genome framework. New genome datasets are included into IMG ER prior to their public release either with their native annotations or with annotations generated by IMG ER's annotation pipeline. IMG ER tools allow addressing annotation problems detected with IMG's comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes.

  2. Human Genome Annotation

    NASA Astrophysics Data System (ADS)

    Gerstein, Mark

    A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes. My talk will focus on annotating the 99% of the genome that does not code for canonical genes, concentrating on intergenic features such as structural variants (SVs), pseudogenes (protein fossils), binding sites, and novel transcribed RNAs (ncRNAs). In particular, I will describe how we identify regulatory sites and variable blocks (SVs) based on processing next-generation sequencing experiments. I will further explain how we cluster together groups of sites to create larger annotations. Next, I will discuss a comprehensive pseudogene identification pipeline, which has enabled us to identify >10K pseudogenes in the genome and analyze their distribution with respect to age, protein family, and chromosomal location. Throughout, I will try to introduce some of the computational algorithms and approaches that are required for genome annotation. Much of this work has been carried out in the framework of the ENCODE, modENCODE, and 1000 genomes projects.

  3. NCBI prokaryotic genome annotation pipeline.

    PubMed

    Tatusova, Tatiana; DiCuccio, Michael; Badretdin, Azat; Chetvernin, Vyacheslav; Nawrocki, Eric P; Zaslavsky, Leonid; Lomsadze, Alexandre; Pruitt, Kim D; Borodovsky, Mark; Ostell, James

    2016-08-19

    Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across the whole domain of prokaryotes. To meet the challenge of timely interpretation of structure, function and meaning of this vast genetic information, a comprehensive approach to automatic genome annotation is critically needed. In collaboration with Georgia Tech, NCBI has developed a new approach to genome annotation that combines alignment based methods with methods of predicting protein-coding and RNA genes and other functional elements directly from sequence. A new gene finding tool, GeneMarkS+, uses the combined evidence of protein and RNA placement by homology as an initial map of annotation to generate and modify ab initio gene predictions across the whole genome. Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence. The pipeline provides a framework for generation and analysis of annotation on the full breadth of prokaryotic taxonomy. For additional information on PGAP see https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ and the NCBI Handbook, https://www.ncbi.nlm.nih.gov/books/NBK174280/. PMID:27342282

  4. Automatic annotation of organellar genomes with DOGMA

    SciTech Connect

    Wyman, Stacia; Jansen, Robert K.; Boore, Jeffrey L.

    2004-06-01

    Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of extra-nuclear organellar (chloroplast and animal mitochondrial) genomes. It is a web-based package that allows the use of comparative BLAST searches to identify and annotate genes in a genome. DOGMA presents a list of putative genes to the user in a graphical format for viewing and editing. Annotations are stored on our password-protected server. Complete annotations can be extracted for direct submission to GenBank. Furthermore, intergenic regions of specified length can be extracted, as well the nucleotide sequences and amino acid sequences of the genes.

  5. Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine

    PubMed Central

    Elsik, Christine G.; Tayal, Aditi; Diesh, Colin M.; Unni, Deepak R.; Emery, Marianne L.; Nguyen, Hung N.; Hagen, Darren E.

    2016-01-01

    We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

  6. Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine.

    PubMed

    Elsik, Christine G; Tayal, Aditi; Diesh, Colin M; Unni, Deepak R; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

    2016-01-01

    We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

  7. JGI Plant Genomics Gene Annotation Pipeline

    SciTech Connect

    Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; Hayes, David; Mitros, Therese

    2014-07-14

    Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.

  8. Genome Annotation and Curation Using MAKER and MAKER-P

    PubMed Central

    Campbell, Michael S.; Holt, Carson; Moore, Barry; Yandell, Mark

    2014-01-01

    This unit describes how to use the genome annotation and curation tools MAKER and MAKER-P to annotate protein coding and non-coding RNA genes in newly assembled genomes, update/combine legacy annotations in light of new evidence, add quality metrics to annotations from other pipelines, and map existing annotations to a new assembly. MAKER and MAKER-P can rapidly annotate genomes of any size, and scale to match available computational resources. PMID:25501943

  9. Annotating Large Genomes With Exact Word Matches

    PubMed Central

    Healy, John; Thomas, Elizabeth E.; Schwartz, Jacob T.; Wigler, Michael

    2003-01-01

    We have developed a tool for rapidly determining the number of exact matches of any word within large, internally repetitive genomes or sets of genomes. Thus we can readily annotate any sequence, including the entire human genome, with the counts of its constituent words. We create a Burrows-Wheeler transform of the genome, which together with auxiliary data structures facilitating counting, can reside in about one gigabyte of RAM. Our original interest was motivated by oligonucleotide probe design, and we describe a general protocol for defining unique hybridization probes. But our method also has applications for the analysis of genome structure and assembly. We demonstrate the identification of chromosome-specific repeats, and outline a general procedure for finding undiscovered repeats. We also illustrate the changing contents of the human genome assemblies by comparing the annotations built from different genome freezes. PMID:12975312

  10. Genome Annotation of Five Mycoplasma canis Strains

    PubMed Central

    May, M.; Michaels, D. L.; Barbet, A. F.

    2012-01-01

    To understand its potential to cause invasive disease, the genome of Mycoplasma canis strain PG14T from a dog's throat was compared to those of isolates from the genital tract or brain of dogs. The average nucleotide identity between strain pairs is 98%, and their genome annotations are similar. PMID:22815452

  11. MicroScope: a platform for microbial genome annotation and comparative genomics

    PubMed Central

    Vallenet, D.; Engelen, S.; Mornico, D.; Cruveiller, S.; Fleury, L.; Lajus, A.; Rouy, Z.; Roche, D.; Salvignol, G.; Scarpelli, C.; Médigue, C.

    2009-01-01

    The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope’s rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of

  12. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    SciTech Connect

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  13. The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes.

    PubMed

    Mavromatis, Konstantinos; Ivanova, Natalia N; Chen, I-Min A; Szeto, Ernest; Markowitz, Victor M; Kyrpides, Nikos C

    2009-01-01

    The DOE-JGI Microbial Annotation Pipeline (DOE-JGI MAP) supports gene prediction and/or functional annotation of microbial genomes towards comparative analysis with the Integrated Microbial Genome (IMG) system. DOE-JGI MAP annotation is applied on nucleotide sequence datasets included in the IMG-ER (Expert Review) version of IMG via the IMG ER submission site. Users can submit the sequence datasets consisting of one or more contigs in a multi-fasta file. DOE-JGI MAP annotation includes prediction of protein coding and RNA genes, as well as repeats and assignment of product names to these genes. PMID:21304638

  14. The DOE-JGI Standard Operating Procedure for the Annotations of the Microbial Genomes

    SciTech Connect

    Mavromatis, Konstantinos; Ivanova, Natalia; Chen, I-Min A.; Szeto, Ernest; Markowitz, Victor; Kyrpides, Nikos C.

    2009-05-20

    The DOE-JGI Microbial Annotation Pipeline (DOE-JGI MAP) supports gene prediction and/or functional annotation of microbial genomes towards comparative analysis with the Integrated Microbial Genome (IMG) system. DOE-JGI MAP annotation is applied on nucleotide sequence datasets included in the IMG-ER (Expert Review) version of IMG via the IMG ER submission site. Users can submit the sequence datasets consisting of one or more contigs in a multi-fasta file. DOE-JGI MAP annotation includes prediction of protein coding and RNA genes, as well as repeats and assignment of product names to these genes.

  15. Genepi: a blackboard framework for genome annotation

    PubMed Central

    Descorps-Declère, Stéphane; Ziébelin, Danielle; Rechenmann, François; Viari, Alain

    2006-01-01

    Background Genome annotation can be viewed as an incremental, cooperative, data-driven, knowledge-based process that involves multiple methods to predict gene locations and structures. This process might have to be executed more than once and might be subjected to several revisions as the biological (new data) or methodological (new methods) knowledge evolves. In this context, although a lot of annotation platforms already exist, there is still a strong need for computer systems which take in charge, not only the primary annotation, but also the update and advance of the associated knowledge. In this paper, we propose to adopt a blackboard architecture for designing such a system Results We have implemented a blackboard framework (called Genepi) for developing automatic annotation systems. The system is not bound to any specific annotation strategy. Instead, the user will specify a blackboard structure in a configuration file and the system will instantiate and run this particular annotation strategy. The characteristics of this framework are presented and discussed. Specific adaptations to the classical blackboard architecture have been required, such as the description of the activation patterns of the knowledge sources by using an extended set of Allen's temporal relations. Although the system is robust enough to be used on real-size applications, it is of primary use to bioinformatics researchers who want to experiment with blackboard architectures. Conclusion In the context of genome annotation, blackboards have several interesting features related to the way methodological and biological knowledge can be updated. They can readily handle the cooperative (several methods are implied) and opportunistic (the flow of execution depends on the state of our knowledge) aspects of the annotation process. PMID:17038181

  16. Functional Annotation Analytics of Rhodopseudomonas palustris Genomes

    PubMed Central

    Simmons, Shaneka S.; Isokpehi, Raphael D.; Brown, Shyretha D.; McAllister, Donee L.; Hall, Charnia C.; McDuffy, Wanaki M.; Medley, Tamara L.; Udensi, Udensi K.; Rajnarayanan, Rajendram V.; Ayensu, Wellington K.; Cohly, Hari H.P.

    2011-01-01

    Rhodopseudomonas palustris, a nonsulphur purple photosynthetic bacteria, has been extensively investigated for its metabolic versatility including ability to produce hydrogen gas from sunlight and biomass. The availability of the finished genome sequences of six R. palustris strains (BisA53, BisB18, BisB5, CGA009, HaA2 and TIE-1) combined with online bioinformatics software for integrated analysis presents new opportunities to determine the genomic basis of metabolic versatility and ecological lifestyles of the bacteria species. The purpose of this investigation was to compare the functional annotations available for multiple R. palustris genomes to identify annotations that can be further investigated for strain-specific or uniquely shared phenotypic characteristics. A total of 2,355 protein family Pfam domain annotations were clustered based on presence or absence in the six genomes. The clustering process identified groups of functional annotations including those that could be verified as strain-specific or uniquely shared phenotypes. For example, genes encoding water/glycerol transport were present in the genome sequences of strains CGA009 and BisB5, but absent in strains BisA53, BisB18, HaA2 and TIE-1. Protein structural homology modeling predicted that the two orthologous 240 aa R. palustris aquaporins have water-specific transport function. Based on observations in other microbes, the presence of aquaporin in R. palustris strains may improve freeze tolerance in natural conditions of rapid freezing such as nitrogen fixation at low temperatures where access to liquid water is a limiting factor for nitrogenase activation. In the case of adaptive loss of aquaporin genes, strains may be better adapted to survive in conditions of high-sugar content such as fermentation of biomass for biohydrogen production. Finally, web-based resources were developed to allow for interactive, user-defined selection of the relationship between protein family annotations and the R

  17. Quantitative measures for the management and comparison of annotated genomes

    PubMed Central

    Eilbeck, Karen; Moore, Barry; Holt, Carson; Yandell, Mark

    2009-01-01

    Background The ever-increasing number of sequenced and annotated genomes has made management of their annotations a significant undertaking, especially for large eukaryotic genomes containing many thousands of genes. Typically, changes in gene and transcript numbers are used to summarize changes from release to release, but these measures say nothing about changes to individual annotations, nor do they provide any means to identify annotations in need of manual review. Results In response, we have developed a suite of quantitative measures to better characterize changes to a genome's annotations between releases, and to prioritize problematic annotations for manual review. We have applied these measures to the annotations of five eukaryotic genomes over multiple releases – H. sapiens, M. musculus, D. melanogaster, A. gambiae, and C. elegans. Conclusion Our results provide the first detailed, historical overview of how these genomes' annotations have changed over the years, and demonstrate the usefulness of these measures for genome annotation management. PMID:19236712

  18. Genomic Data and Annotation from the SEED

    DOE Data Explorer

    Fonstein, Michael; Kogan, Yakov; Osterman, Andrei; Overbeek, Ross; Vonstein, Veronika The Fellowship for Interpretation of Genomes (FIG)

    The SEED Project is a cooperative effort to annotate ever-expanding genomic data so researchers can conduct effective comparative analyses of genomes. Launched in 2003 by the Fellowship for Interpretation of Genomes (FIG), the project is one of several initiatives in ongoing development of data curation systems. SEED is designed to be used by scientists from numerous centers and with varied research objectives. As such, several institutions have since joined FIG in a consortium, including the University of Chicago, DOE’s Argonne National Laboratory (ANL), the University of Illinois at Urbana-Champaign, and others. As one example, ANL has used SEED to develop the National Microbial Pathogen Data Resource. Other agencies and institutions have used the project to discover genome components and clarify gene functions such as metabolism. SEED also has enabled researchers to conduct comparative analyses of closely related genomes and has supported derivation of stoichiometric models to understand metabolic processes. The SEED Project has been extended to support metagenomic samples and concomitant analytical tools. Moreover, the number of genomes being introduced into SEED is growing very rapidly. Building a framework to support this growth while providing highly accurate annotations is centrally important to SEED. The project’s subsystem-based annotation strategy has become the technological foundation for addressing these challenges.(copied from Appendix 7 of Systems Biology Knowledgebase for a New Era in Biology, A Genomics:GTL Report from the May 2008 Workshop, DOE/SC-0113, Grequrick, S; Fredrickson, J.K.; Stevens, R., Pub March 1, 2009.)

  19. Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics

    PubMed Central

    Dodhia, Kejal; Stoll, Thomas; Hastie, Marcus; Furuki, Eiko; Ellwood, Simon R.; Williams, Angela H.; Tan, Yew-Foon; Testa, Alison C.; Gorman, Jeffrey J.; Oliver, Richard P.

    2016-01-01

    Parastagonospora nodorum, the causal agent of Septoria nodorum blotch (SNB), is an economically important pathogen of wheat (Triticum spp.), and a model for the study of necrotrophic pathology and genome evolution. The reference P. nodorum strain SN15 was the first Dothideomycete with a published genome sequence, and has been used as the basis for comparison within and between species. Here we present an updated reference genome assembly with corrections of SNP and indel errors in the underlying genome assembly from deep resequencing data as well as extensive manual annotation of gene models using transcriptomic and proteomic sources of evidence (https://github.com/robsyme/Parastagonospora_nodorum_SN15). The updated assembly and annotation includes 8,366 genes with modified protein sequence and 866 new genes. This study shows the benefits of using a wide variety of experimental methods allied to expert curation to generate a reliable set of gene models. PMID:26840125

  20. Linking genome-scale metabolic modeling and genome annotation

    PubMed Central

    Blais, Edik M.; Chavali, Arvind K.; Papin, Jason A.

    2014-01-01

    Summary Genome-scale metabolic network reconstructions, assembled from annotated genomes, serve as a platform for integrating data from heterogeneous sources and generating hypotheses for further experimental validation. Implementing constraint-based modeling techniques such as Flux Balance Analysis (FBA) on network reconstructions allow for interrogating metabolism at a systems-level, which aids in identifying and rectifying gaps in knowledge. With genome sequences for various organisms from prokaryotes to eukaryotes becoming increasingly available, a significant bottleneck lies in the structural and functional annotation of these sequences. Using topologically-based and biologically-inspired metabolic network refinement, we can better characterize enzymatic functions present in an organism and link annotation of these functions to candidate transcripts, both steps that can be experimentally validated. PMID:23417799

  1. TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.

    PubMed

    Leroy, Philippe; Guilhot, Nicolas; Sakai, Hiroaki; Bernard, Aurélien; Choulet, Frédéric; Theil, Sébastien; Reboux, Sébastien; Amano, Naoki; Flutre, Timothée; Pelegrin, Céline; Ohyanagi, Hajime; Seidel, Michael; Giacomoni, Franck; Reichstadt, Mathieu; Alaux, Michael; Gicquello, Emmanuelle; Legeai, Fabrice; Cerutti, Lorenzo; Numa, Hisataka; Tanaka, Tsuyoshi; Mayer, Klaus; Itoh, Takeshi; Quesneville, Hadi; Feuillet, Catherine

    2012-01-01

    In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future. PMID:22645565

  2. Descartes' fly: the geometry of genomic annotation.

    PubMed

    Kim, J

    2001-03-01

    The completion of the Drosophila melanogaster genome marks another significant milestone in the growth of sequence information. But it also contributes to the ever-widening gap between sequence information and biological knowledge. One important approach to reducing this gap is theoretical inference through computational technologies. Many computer programs have been designed to annotate genomic sequence information with biologically relevant information. Here, I suggest that all of these methods have a common structure in which the sequence fragments are "coordinated" by some method of description such as Hidden Markov models. The key to the algorithms lies in constructing the most efficient set of coordinates that allow extrapolation and interpolation from existing knowledge. Efficient extrapolation and interpolation are produced if the sequence fragments acquire a natural geometrical structure in the coordinated description. Finding such a coordinate frame is an inductive problem with no algorithmic solution. The greater part of the problem of genomic annotation lies in biological modeling of the data rather than in algorithmic improvements. PMID:11793243

  3. Towards a Library of Standard Operating Procedures (SOPs) for (meta)genomic annotation

    SciTech Connect

    Kyrpides, Nikos; Angiuoli, Samuel V.; Cochrane, Guy; Field, Dawn; Garrity, George; Gussman, Aaron; Kodira, Chinnappa D.; Klimke, William; Kyrpides, Nikos; Madupu, Ramana; Markowitz, Victor; Tatusova, Tatiana; Thomson, Nick; White, Owen

    2008-04-01

    Genome annotations describe the features of genomes and accompany sequences in genome databases. The methodologies used to generate genome annotation are diverse and typically vary amongst groups. Descriptions of the annotation procedure are helpful in interpreting genome annotation data. Standard Operating Procedures (SOPs) for genome annotation describe the processes that generate genome annotations. Some groups are currently documenting procedures but standards are lacking for structure and content of annotation SOPs. In addition, there is no central repository to store and disseminate procedures and protocols for genome annotation. We highlight the importance of SOPs for genome annotation and endorse a central online repository of SOPs.

  4. ASAP, a systematic annotation package for community analysis of genomes.

    PubMed

    Glasner, Jeremy D; Liss, Paul; Plunkett, Guy; Darling, Aaron; Prasad, Tejasvini; Rusch, Michael; Byrnes, Alexis; Gilson, Michael; Biehl, Bryan; Blattner, Frederick R; Perna, Nicole T

    2003-01-01

    ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and functional characterization (https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm). ASAP facilitates ongoing community annotation of genomes and tracking of information as genome projects move from preliminary data collection through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. ASAP supports three levels of users: public viewers, annotators and curators. Public viewers can currently browse updated annotation information for Escherichia coli K-12 strain MG1655, genome-wide transcript profiles from more than 50 microarray experiments and an extensive collection of mutant strains and associated phenotypic data. Annotators worldwide are currently using ASAP to participate in a community annotation project for the Erwinia chrysanthemi strain 3937 genome. Curation of the E. chrysanthemi genome annotation as well as those of additional published enterobacterial genomes is underway and will be publicly accessible in the near future. PMID:12519969

  5. Genome-wide metabolic (re-) annotation of Kluyveromyces lactis

    PubMed Central

    2012-01-01

    Background Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. Research on Kluyveromyces lactis is quite advanced and this yeast species is one of the few with which it is possible to perform formal genetic analysis. Nevertheless, until now, no complete metabolic functional annotation has been performed to the proteins encoded in the Kluyveromyces lactis genome. Results In this work, a new metabolic genome-wide functional re-annotation of the proteins encoded in the Kluyveromyces lactis genome was performed, resulting in the annotation of 1759 genes with metabolic functions, and the development of a methodology supported by merlin (software developed in-house). The new annotation includes novelties, such as the assignment of transporter superfamily numbers to genes identified as transporter proteins. Thus, the genes annotated with metabolic functions could be exclusively enzymatic (1410 genes), transporter proteins encoding genes (301 genes) or have both metabolic activities (48 genes). The new annotation produced by this work largely surpassed the Kluyveromyces lactis currently available annotations. A comparison with KEGG’s annotation revealed a match with 844 (~90%) of the genes annotated by KEGG, while adding 850 new gene annotations. Moreover, there are 32 genes with annotations different from KEGG. Conclusions The methodology developed throughout this work can be used to re-annotate any yeast or, with a little tweak of the reference organism, the proteins encoded in any sequenced genome. The new annotation provided by this study offers basic knowledge which might be useful for the scientific community working on this model yeast, because new functions have been identified for the so-called metabolic genes. Furthermore, it served as the basis for the reconstruction of a compartmentalized, genome-scale metabolic model of Kluyveromyces lactis, which is

  6. Correction of the Caulobacter crescentus NA1000 Genome Annotation

    PubMed Central

    Ely, Bert; Scott, LaTia Etheredge

    2014-01-01

    Bacterial genome annotations are accumulating rapidly in the GenBank database and the use of automated annotation technologies to create these annotations has become the norm. However, these automated methods commonly result in a small, but significant percentage of genome annotation errors. To improve accuracy and reliability, we analyzed the Caulobacter crescentus NA1000 genome utilizing computer programs Artemis and MICheck to manually examine the third codon position GC content, alignment to a third codon position GC frame plot peak, and matches in the GenBank database. We identified 11 new genes, modified the start site of 113 genes, and changed the reading frame of 38 genes that had been incorrectly annotated. Furthermore, our manual method of identifying protein-coding genes allowed us to remove 112 non-coding regions that had been designated as coding regions. The improved NA1000 genome annotation resulted in a reduction in the use of rare codons since noncoding regions with atypical codon usage were removed from the annotation and 49 new coding regions were added to the annotation. Thus, a more accurate codon usage table was generated as well. These results demonstrate that a comparison of the location of peaks third codon position GC content to the location of protein coding regions could be used to verify the annotation of any genome that has a GC content that is greater than 60%. PMID:24621776

  7. Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation.

    PubMed

    Beijbom, Oscar; Edmunds, Peter J; Roelfsema, Chris; Smith, Jennifer; Kline, David I; Neal, Benjamin P; Dunlap, Matthew J; Moriarty, Vincent; Fan, Tung-Yung; Tan, Chih-Jui; Chan, Stephen; Treibitz, Tali; Gamst, Anthony; Mitchell, B Greg; Kriegman, David

    2015-01-01

    Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys. PMID:26154157

  8. Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation

    PubMed Central

    Beijbom, Oscar; Edmunds, Peter J.; Roelfsema, Chris; Smith, Jennifer; Kline, David I.; Neal, Benjamin P.; Dunlap, Matthew J.; Moriarty, Vincent; Fan, Tung-Yung; Tan, Chih-Jui; Chan, Stephen; Treibitz, Tali; Gamst, Anthony; Mitchell, B. Greg; Kriegman, David

    2015-01-01

    Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys. PMID:26154157

  9. Meeting report: a workshop on Best Practices in Genome Annotation

    PubMed Central

    Madupu, Ramana; Brinkac, Lauren M.; Harrow, Jennifer; Wilming, Laurens G.; Böhme, Ulrike; Lamesch, Philippe; Hannick, Linda I.

    2010-01-01

    Efforts to annotate the genomes of a wide variety of model organisms are currently carried out by sequencing centers, model organism databases and academic/institutional laboratories around the world. Different annotation methods and tools have been developed over time to meet the needs of biologists faced with the task of annotating biological data. While standardized methods are essential for consistent curation within each annotation group, methods and tools can differ between groups, especially when the groups are curating different organisms. Biocurators from several institutes met at the Third International Biocuration Conference in Berlin, Germany, April 2009 and hosted the ‘Best Practices in Genome Annotation: Inference from Evidence’ workshop to share their strategies, pipelines, standards and tools. This article documents the material presented in the workshop. PMID:20428316

  10. The 2008 update of the Aspergillus nidulans genome annotation: a community effort

    PubMed Central

    Wortman, Jennifer Russo; Gilsenan, Jane Mabey; Joardar, Vinita; Deegan, Jennifer; Clutterbuck, John; Andersen, Mikael R.; Archer, David; Bencina, Mojca; Braus, Gerhard; Coutinho, Pedro; von Döhren, Hans; Doonan, John; Driessen, Arnold J.M.; Durek, Pawel; Espeso, Eduardo; Fekete, Erzsébet; Flipphi, Michel; Estrada, Carlos Garcia; Geysens, Steven; Goldman, Gustavo; de Groot, Piet W.J.; Hansen, Kim; Harris, Steven D.; Heinekamp, Thorsten; Helmstaedt, Kerstin; Henrissat, Bernard; Hofmann, Gerald; Homan, Tim; Horio, Tetsuya; Horiuchi, Hiroyuki; James, Steve; Jones, Meriel; Karaffa, Levente; Karányi, Zsolt; Kato, Masashi; Keller, Nancy; Kelly, Diane E.; Kiel, Jan A.K.W.; Kim, Jung-Mi; van der Klei, Ida J.; Klis, Frans M.; Kovalchuk, Andriy; Kraševec, Nada; Kubicek, Christian P.; Liu, Bo; MacCabe, Andrew; Meyer, Vera; Mirabito, Pete; Miskei, Márton; Mos, Magdalena; Mullins, Jonathan; Nelson, David R.; Nielsen, Jens; Oakley, Berl R.; Osmani, Stephen A.; Pakula, Tiina; Paszewski, Andrzej; Paulsen, Ian; Pilsyk, Sebastian; Pócsi, István; Punt, Peter J.; Ram, Arthur F.J.; Ren, Qinghu; Robellet, Xavier; Robson, Geoff; Seiboth, Bernhard; Solingen, Piet van; Specht, Thomas; Sun, Jibin; Taheri-Talesh, Naimeh; Takeshita, Norio; Ussery, Dave; vanKuyk, Patricia A.; Visser, Hans; van de Vondervoort, Peter J.I.; de Vries, Ronald P.; Walton, Jonathan; Xiang, Xin; Xiong, Yi; Zeng, An Ping; Brandt, Bernd W.; Cornell, Michael J.; van den Hondel, Cees A.M.J.J.; Visser, Jacob; Oliver, Stephen G.; Turner, Geoffrey

    2010-01-01

    The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology. PMID:19146970

  11. Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

    SciTech Connect

    Rutledge, Alexandra C.; Jones, Marcus B.; Chauhan, Sadhana; Purvine, Samuel O.; Sanford, James; Monroe, Matthew E.; Brewer, Heather M.; Payne, Samuel H.; Ansong, Charles; Frank, Bryan C.; Smith, Richard D.; Peterson, Scott; Motin, Vladimir L.; Adkins, Joshua N.

    2012-03-27

    Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. To date, the perceived value of manual curation for genome annotations is not offset by the real cost and time associated with the process. In order to balance the large number of sequences generated, the annotation process is now performed almost exclusively in an automated fashion for most genome sequencing projects. One possible way to reduce errors inherent to automated computational annotations is to apply data from 'omics' measurements (i.e. transcriptional and proteomic) to the un-annotated genome with a proteogenomic-based approach. This approach does require additional experimental and bioinformatics methods to include omics technologies; however, the approach is readily automatable and can benefit from rapid developments occurring in those research domains as well. The annotation process can be improved by experimental validation of transcription and translation and aid in the discovery of annotation errors. Here the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species, as is becoming common in sequencing efforts. Transcriptomic and proteomic data derived from three highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis pestoides F, and Y. pseudotuberculosis PB1/+) was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 previously incorrect protein-coding sequences (e.g., observed frameshifts, extended start sites, and translated pseudogenes) within the three current Yersinia genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent pathogen, thus

  12. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

    SciTech Connect

    Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, III, James A.; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang

    2015-02-10

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

  13. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

    PubMed Central

    Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, James A.; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang

    2015-01-01

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception. PMID:25666585

  14. xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud.

    PubMed

    Duvick, Jon; Standage, Daniel S; Merchant, Nirav; Brendel, Volker P

    2016-04-01

    Genome-wide annotation of gene structure requires the integration of numerous computational steps. Currently, annotation is arguably best accomplished through collaboration of bioinformatics and domain experts, with broad community involvement. However, such a collaborative approach is not scalable at today's pace of sequence generation. To address this problem, we developed the xGDBvm software, which uses an intuitive graphical user interface to access a number of common genome analysis and gene structure tools, preconfigured in a self-contained virtual machine image. Once their virtual machine instance is deployed through iPlant's Atmosphere cloud services, users access the xGDBvm workflow via a unified Web interface to manage inputs, set program parameters, configure links to high-performance computing (HPC) resources, view and manage output, apply analysis and editing tools, or access contextual help. The xGDBvm workflow will mask the genome, compute spliced alignments from transcript and/or protein inputs (locally or on a remote HPC cluster), predict gene structures and gene structure quality, and display output in a public or private genome browser complete with accessory tools. Problematic gene predictions are flagged and can be reannotated using the integrated yrGATE annotation tool. xGDBvm can also be configured to append or replace existing data or load precomputed data. Multiple genomes can be annotated and displayed, and outputs can be archived for sharing or backup. xGDBvm can be adapted to a variety of use cases including de novo genome annotation, reannotation, comparison of different annotations, and training or teaching. PMID:27020957

  15. Rapid reconstruction and annotation of vaccinium macrocarpon organellar genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The mitochondria genome of the American cranberry (Vaccinium macrocarpon Ait.) cultivar “HyRed” is being reconstructed using sequence 454 shotgun data and in silico procedures. We previously reconstructed and annotated a putative plastid cranberry genome with an approximate length of 176kb. The reli...

  16. Machine learning and genome annotation: a match meant to be?

    PubMed Central

    2013-01-01

    By its very nature, genomics produces large, high-dimensional datasets that are well suited to analysis by machine learning approaches. Here, we explain some key aspects of machine learning that make it useful for genome annotation, with illustrative examples from ENCODE. PMID:23731483

  17. Annotation of the Protein Coding Regions of the Equine Genome

    PubMed Central

    Hestand, Matthew S.; Kalbfleisch, Theodore S.; Coleman, Stephen J.; Zeng, Zheng; Liu, Jinze; Orlando, Ludovic; MacLeod, James N.

    2015-01-01

    Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced mRNA from a pool of forty-three different tissues. From these, we derived the structures of 68,594 transcripts. In addition, we identified 301,829 positions with SNPs or small indels within these transcripts relative to EquCab2. Interestingly, 780 variants extend the open reading frame of the transcript and appear to be small errors in the equine reference genome, since they are also identified as homozygous variants by genomic DNA resequencing of the reference horse. Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross-species transcriptional and genomic comparisons. PMID:26107351

  18. Scripps Genome ADVISER: Annotation and Distributed Variant Interpretation SERver

    PubMed Central

    Pham, Phillip H.; Shipman, William J.; Erikson, Galina A.; Schork, Nicholas J.; Torkamani, Ali

    2015-01-01

    Interpretation of human genomes is a major challenge. We present the Scripps Genome ADVISER (SG-ADVISER) suite, which aims to fill the gap between data generation and genome interpretation by performing holistic, in-depth, annotations and functional predictions on all variant types and effects. The SG-ADVISER suite includes a de-identification tool, a variant annotation web-server, and a user interface for inheritance and annotation-based filtration. SG-ADVISER allows users with no bioinformatics expertise to manipulate large volumes of variant data with ease – without the need to download large reference databases, install software, or use a command line interface. SG-ADVISER is freely available at genomics.scripps.edu/ADVISER. PMID:25706643

  19. Genome and proteome annotation: organization, interpretation and integration

    PubMed Central

    Reeves, Gabrielle A.; Talavera, David; Thornton, Janet M.

    2008-01-01

    Recent years have seen a huge increase in the generation of genomic and proteomic data. This has been due to improvements in current biological methodologies, the development of new experimental techniques and the use of computers as support tools. All these raw data are useless if they cannot be properly analysed, annotated, stored and displayed. Consequently, a vast number of resources have been created to present the data to the wider community. Annotation tools and databases provide the means to disseminate these data and to comprehend their biological importance. This review examines the various aspects of annotation: type, methodology and availability. Moreover, it puts a special interest on novel annotation fields, such as that of phenotypes, and highlights the recent efforts focused on the integrating annotations. PMID:19019817

  20. OMIGA: Optimized Maker-Based Insect Genome Annotation.

    PubMed

    Liu, Jinding; Xiao, Huamei; Huang, Shuiqing; Li, Fei

    2014-08-01

    Insects are one of the largest classes of animals on Earth and constitute more than half of all living species. The i5k initiative has begun sequencing of more than 5,000 insect genomes, which should greatly help in exploring insect resource and pest control. Insect genome annotation remains challenging because many insects have high levels of heterozygosity. To improve the quality of insect genome annotation, we developed a pipeline, named Optimized Maker-Based Insect Genome Annotation (OMIGA), to predict protein-coding genes from insect genomes. We first mapped RNA-Seq reads to genomic scaffolds to determine transcribed regions using Bowtie, and the putative transcripts were assembled using Cufflink. We then selected highly reliable transcripts with intact coding sequences to train de novo gene prediction software, including Augustus. The re-trained software was used to predict genes from insect genomes. Exonerate was used to refine gene structure and to determine near exact exon/intron boundary in the genome. Finally, we used the software Maker to integrate data from RNA-Seq, de novo gene prediction, and protein alignment to produce an official gene set. The OMIGA pipeline was used to annotate the draft genome of an important insect pest, Chilo suppressalis, yielding 12,548 genes. Different strategies were compared, which demonstrated that OMIGA had the best performance. In summary, we present a comprehensive pipeline for identifying genes in insect genomes that can be widely used to improve the annotation quality in insects. OMIGA is provided at http://ento.njau.edu.cn/omiga.html . PMID:24609470

  1. EGASP: the human ENCODE Genome Annotation Assessment Project

    PubMed Central

    Guigó, Roderic; Flicek, Paul; Abril, Josep F; Reymond, Alexandre; Lagarde, Julien; Denoeud, France; Antonarakis, Stylianos; Ashburner, Michael; Bajic, Vladimir B; Birney, Ewan; Castelo, Robert; Eyras, Eduardo; Ucla, Catherine; Gingeras, Thomas R; Harrow, Jennifer; Hubbard, Tim; Lewis, Suzanna E; Reese, Martin G

    2006-01-01

    Background We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a 'reference set' of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment. Results The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could be verified. Conclusion This is the first such experiment in human DNA, and we have followed the standards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe the results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence. PMID:16925836

  2. Genome sequencing and annotation of Serratia sp. strain TEL.

    PubMed

    Lephoto, Tiisetso E; Gray, Vincent M

    2015-12-01

    We present the annotation of the draft genome sequence of Serratia sp. strain TEL (GenBank accession number KP711410). This organism was isolated from entomopathogenic nematode Oscheius sp. strain TEL (GenBank accession number KM492926) collected from grassland soil and has a genome size of 5,000,541 bp and 542 subsystems. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession number LDEG00000000. PMID:26697332

  3. Applying negative rule mining to improve genome annotation

    PubMed Central

    Artamonova, Irena I; Frishman, Goar; Frishman, Dmitrij

    2007-01-01

    Background Unsupervised annotation of proteins by software pipelines suffers from very high error rates. Spurious functional assignments are usually caused by unwarranted homology-based transfer of information from existing database entries to the new target sequences. We have previously demonstrated that data mining in large sequence annotation databanks can help identify annotation items that are strongly associated with each other, and that exceptions from strong positive association rules often point to potential annotation errors. Here we investigate the applicability of negative association rule mining to revealing erroneously assigned annotation items. Results Almost all exceptions from strong negative association rules are connected to at least one wrong attribute in the feature combination making up the rule. The fraction of annotation features flagged by this approach as suspicious is strongly enriched in errors and constitutes about 0.6% of the whole body of the similarity-transferred annotation in the PEDANT genome database. Positive rule mining does not identify two thirds of these errors. The approach based on exceptions from negative rules is much more specific than positive rule mining, but its coverage is significantly lower. Conclusion Mining of both negative and positive association rules is a potent tool for finding significant trends in protein annotation and flagging doubtful features for further inspection. PMID:17659089

  4. A Manual Curation Strategy to Improve Genome Annotation: Application to a Set of Haloarchael Genomes

    PubMed Central

    Pfeiffer, Friedhelm; Oesterhelt, Dieter

    2015-01-01

    Genome annotation errors are a persistent problem that impede research in the biosciences. A manual curation effort is described that attempts to produce high-quality genome annotations for a set of haloarchaeal genomes (Halobacterium salinarum and Hbt. hubeiense, Haloferax volcanii and Hfx. mediterranei, Natronomonas pharaonis and Nmn. moolapensis, Haloquadratum walsbyi strains HBSQ001 and C23, Natrialba magadii, Haloarcula marismortui and Har. hispanica, and Halohasta litchfieldiae). Genomes are checked for missing genes, start codon misassignments, and disrupted genes. Assignments of a specific function are preferably based on experimentally characterized homologs (Gold Standard Proteins). To avoid overannotation, which is a major source of database errors, we restrict annotation to only general function assignments when support for a specific substrate assignment is insufficient. This strategy results in annotations that are resistant to the plethora of errors that compromise public databases. Annotation consistency is rigorously validated for ortholog pairs from the genomes surveyed. The annotation is regularly crosschecked against the UniProt database to further improve annotations and increase the level of standardization. Enhanced genome annotations are submitted to public databases (EMBL/GenBank, UniProt), to the benefit of the scientific community. The enhanced annotations are also publically available via HaloLex. PMID:26042526

  5. GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.

    PubMed

    Gremme, Gordon; Steinbiss, Sascha; Kurtz, Stefan

    2013-01-01

    Genome annotations are often published as plain text files describing genomic features and their subcomponents by an implicit annotation graph. In this paper, we present the GenomeTools, a convenient and efficient software library and associated software tools for developing bioinformatics software intended to create, process or convert annotation graphs. The GenomeTools strictly follow the annotation graph approach, offering a unified graph-based representation. This gives the developer intuitive and immediate access to genomic features and tools for their manipulation. To process large annotation sets with low memory overhead, we have designed and implemented an efficient pull-based approach for sequential processing of annotations. This allows to handle even the largest annotation sets, such as a complete catalogue of human variations. Our object-oriented C-based software library enables a developer to conveniently implement their own functionality on annotation graphs and to integrate it into larger workflows, simultaneously accessing compressed sequence data if required. The careful C implementation of the GenomeTools does not only ensure a light-weight memory footprint while allowing full sequential as well as random access to the annotation graph, but also facilitates the creation of bindings to a variety of script programming languages (like Python and Ruby) sharing the same interface. PMID:24091398

  6. Comparative genomics and functional annotation of bacterial transporters

    NASA Astrophysics Data System (ADS)

    Gelfand, Mikhail S.; Rodionov, Dmitry A.

    2008-03-01

    Transport proteins are difficult to study experimentally, and because of that their functional characterization trails that of enzymes. The comparative genomic analysis is a powerful approach to functional annotation of proteins, which makes it possible to utilize the genomic sequence data from thousands of organisms. The use of computational techniques allows one to identify candidate transporters, predict their structure and localization in the membrane, and perform detailed functional annotation, which includes substrate specificity and cellular role. We overview the main techniques of analysis of transporters' structure and function. We consider the most popular algorithms to identify transmembrane segments in protein sequences and to predict topology of multispanning proteins. We describe the main approaches of the comparative genomics, and how they may be applied to the analysis of transporters, and provide examples showing how combinations of these techniques is used for functional annotation of new transporter specificities in known families, characterization of new families, and prediction of novel transport mechanisms.

  7. Towards the VWO Annotation Service: a Success Story of the IMAGE RPI Expert Rating System

    NASA Astrophysics Data System (ADS)

    Reinisch, B. W.; Galkin, I. A.; Fung, S. F.; Benson, R. F.; Kozlov, A. V.; Khmyrov, G. M.; Garcia, L. N.

    2010-12-01

    Interpretation of Heliophysics wave data requires specialized knowledge of wave phenomena. Users of the virtual wave observatory (VWO) will greatly benefit from a data annotation service that will allow querying of data by phenomenon type, thus helping accomplish the VWO goal to make Heliophysics wave data searchable, understandable, and usable by the scientific community. Individual annotations can be sorted by phenomenon type and reduced into event lists (catalogs). However, in contrast to the event lists, annotation records allow a greater flexibility of collaborative management by more easily admitting operations of addition, revision, or deletion. They can therefore become the building blocks for an interactive Annotation Service with a suitable graphic user interface to the VWO middleware. The VWO Annotation Service vision is an interactive, collaborative sharing of domain expert knowledge with fellow scientists and students alike. An effective prototype of the VWO Annotation Service has been in operation at the University of Massachusetts Lowell since 2001. An expert rating system (ERS) was developed for annotating the IMAGE radio plasma imager (RPI) active sounding data containing 1.2 million plasmagrams. The RPI data analysts can use ERS to submit expert ratings of plasmagram features, such as presence of echo traces resulted from reflected RPI signals from distant plasma structures. Since its inception in 2001, the RPI ERS has accumulated 7351 expert plasmagram ratings in 16 phenomenon categories, together with free-text descriptions and other metadata. In addition to human expert ratings, the system holds 225,125 ratings submitted by the CORPRAL data prospecting software that employs a model of the human pre-attentive vision to select images potentially containing interesting features. The annotation records proved to be instrumental in a number of investigations where manual data exploration would have been prohibitively tedious and expensive

  8. Genome annotation of a Saccharomyces sp. lager brewer's yeast.

    PubMed

    De León-Medina, Patricia Marcela; Elizondo-González, Ramiro; Damas-Buenrostro, Luis Cástulo; Geertman, Jan-Maarten; Van den Broek, Marcel; Galán-Wong, Luis Jesús; Ortiz-López, Rocío; Pereyra-Alférez, Benito

    2016-09-01

    The genome of lager brewer's yeast is a hybrid, with Saccharomyces eubayanus and Saccharomyces cerevisiae as sub-genomes. Due to their specific use in the beer industry, relatively little information is available. The genome of brewing yeast was sequenced and annotated in this study. We obtained a genome size of 22.7 Mbp that consisted of 133 scaffolds, with 65 scaffolds larger than 10 kbp. With respect to the annotation, 9939 genes were obtained, and when they were submitted to a local alignment, we found that 53.93% of these genes corresponded to S. cerevisiae, while another 42.86% originated from S. eubayanus. Our results confirm that our strain is a hybrid of at least two different genomes. PMID:27330999

  9. Intra-species sequence comparisons for annotating genomes

    SciTech Connect

    Boffelli, Dario; Weer, Claire V.; Weng, Li; Lewis, Keith D.; Shoukry, Malak I.; Pachter, Lior; Keys, David N.; Rubin, Edward M.

    2004-07-15

    Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intra-species sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents and a set of genomic intervals amplified, resequenced and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom and raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species. The sequence data from this study has been submitted to GenBank under accession nos. AY667278-AY667407.

  10. GENCODE: The reference human genome annotation for The ENCODE Project

    PubMed Central

    Harrow, Jennifer; Frankish, Adam; Gonzalez, Jose M.; Tapanari, Electra; Diekhans, Mark; Kokocinski, Felix; Aken, Bronwen L.; Barrell, Daniel; Zadissa, Amonida; Searle, Stephen; Barnes, If; Bignell, Alexandra; Boychenko, Veronika; Hunt, Toby; Kay, Mike; Mukherjee, Gaurab; Rajan, Jeena; Despacio-Reyes, Gloria; Saunders, Gary; Steward, Charles; Harte, Rachel; Lin, Michael; Howald, Cédric; Tanzer, Andrea; Derrien, Thomas; Chrast, Jacqueline; Walters, Nathalie; Balasubramanian, Suganthi; Pei, Baikang; Tress, Michael; Rodriguez, Jose Manuel; Ezkurdia, Iakes; van Baren, Jeltje; Brent, Michael; Haussler, David; Kellis, Manolis; Valencia, Alfonso; Reymond, Alexandre; Gerstein, Mark; Guigó, Roderic; Hubbard, Tim J.

    2012-01-01

    The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers. PMID:22955987

  11. GENCODE: the reference human genome annotation for The ENCODE Project.

    PubMed

    Harrow, Jennifer; Frankish, Adam; Gonzalez, Jose M; Tapanari, Electra; Diekhans, Mark; Kokocinski, Felix; Aken, Bronwen L; Barrell, Daniel; Zadissa, Amonida; Searle, Stephen; Barnes, If; Bignell, Alexandra; Boychenko, Veronika; Hunt, Toby; Kay, Mike; Mukherjee, Gaurab; Rajan, Jeena; Despacio-Reyes, Gloria; Saunders, Gary; Steward, Charles; Harte, Rachel; Lin, Michael; Howald, Cédric; Tanzer, Andrea; Derrien, Thomas; Chrast, Jacqueline; Walters, Nathalie; Balasubramanian, Suganthi; Pei, Baikang; Tress, Michael; Rodriguez, Jose Manuel; Ezkurdia, Iakes; van Baren, Jeltje; Brent, Michael; Haussler, David; Kellis, Manolis; Valencia, Alfonso; Reymond, Alexandre; Gerstein, Mark; Guigó, Roderic; Hubbard, Tim J

    2012-09-01

    The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers. PMID:22955987

  12. Web Apollo: a web-based genomic annotation editing platform

    PubMed Central

    2013-01-01

    Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world. PMID:24000942

  13. Expert system for computer-assisted annotation of MS/MS spectra.

    PubMed

    Neuhauser, Nadin; Michalski, Annette; Cox, Jürgen; Mann, Matthias

    2012-11-01

    An important step in mass spectrometry (MS)-based proteomics is the identification of peptides by their fragment spectra. Regardless of the identification score achieved, almost all tandem-MS (MS/MS) spectra contain remaining peaks that are not assigned by the search engine. These peaks may be explainable by human experts but the scale of modern proteomics experiments makes this impractical. In computer science, Expert Systems are a mature technology to implement a list of rules generated by interviews with practitioners. We here develop such an Expert System, making use of literature knowledge as well as a large body of high mass accuracy and pure fragmentation spectra. Interestingly, we find that even with high mass accuracy data, rule sets can quickly become too complex, leading to over-annotation. Therefore we establish a rigorous false discovery rate, calculated by random insertion of peaks from a large collection of other MS/MS spectra, and use it to develop an optimized knowledge base. This rule set correctly annotates almost all peaks of medium or high abundance. For high resolution HCD data, median intensity coverage of fragment peaks in MS/MS spectra increases from 58% by search engine annotation alone to 86%. The resulting annotation performance surpasses a human expert, especially on complex spectra such as those of larger phosphorylated peptides. Our system is also applicable to high resolution collision-induced dissociation data. It is available both as a part of MaxQuant and via a webserver that only requires an MS/MS spectrum and the corresponding peptides sequence, and which outputs publication quality, annotated MS/MS spectra (www.biochem.mpg.de/mann/tools/). It provides expert knowledge to beginners in the field of MS-based proteomics and helps advanced users to focus on unusual and possibly novel types of fragment ions. PMID:22888147

  14. Expert System for Computer-assisted Annotation of MS/MS Spectra*

    PubMed Central

    Neuhauser, Nadin; Michalski, Annette; Cox, Jürgen; Mann, Matthias

    2012-01-01

    An important step in mass spectrometry (MS)-based proteomics is the identification of peptides by their fragment spectra. Regardless of the identification score achieved, almost all tandem-MS (MS/MS) spectra contain remaining peaks that are not assigned by the search engine. These peaks may be explainable by human experts but the scale of modern proteomics experiments makes this impractical. In computer science, Expert Systems are a mature technology to implement a list of rules generated by interviews with practitioners. We here develop such an Expert System, making use of literature knowledge as well as a large body of high mass accuracy and pure fragmentation spectra. Interestingly, we find that even with high mass accuracy data, rule sets can quickly become too complex, leading to over-annotation. Therefore we establish a rigorous false discovery rate, calculated by random insertion of peaks from a large collection of other MS/MS spectra, and use it to develop an optimized knowledge base. This rule set correctly annotates almost all peaks of medium or high abundance. For high resolution HCD data, median intensity coverage of fragment peaks in MS/MS spectra increases from 58% by search engine annotation alone to 86%. The resulting annotation performance surpasses a human expert, especially on complex spectra such as those of larger phosphorylated peptides. Our system is also applicable to high resolution collision-induced dissociation data. It is available both as a part of MaxQuant and via a webserver that only requires an MS/MS spectrum and the corresponding peptides sequence, and which outputs publication quality, annotated MS/MS spectra (www.biochem.mpg.de/mann/tools/). It provides expert knowledge to beginners in the field of MS-based proteomics and helps advanced users to focus on unusual and possibly novel types of fragment ions. PMID:22888147

  15. Improving Genome Assemblies and Annotations for Nonhuman Primates

    PubMed Central

    Norgren, Robert B.

    2013-01-01

    The study of nonhuman primates (NHP) is key to understanding human evolution, in addition to being an important model for biomedical research. NHPs are especially important for translational medicine. There are now exciting opportunities to greatly increase the utility of these models by incorporating Next Generation (NextGen) sequencing into study design. Unfortunately, the draft status of nonhuman genomes greatly constrains what can currently be accomplished with available technology. Although all genomes contain errors, draft assemblies and annotations contain so many mistakes that they make currently available nonhuman primate genomes misleading to investigators conducting evolutionary studies; and these genomes are of insufficient quality to serve as references for NextGen studies. Fortunately, NextGen sequencing can be used in the production of greatly improved genomes. Existing Sanger sequences can be supplemented with NextGen whole genome, and exomic genomic sequences to create new, more complete and correct assemblies. Additional physical mapping, and an incorporation of information about gene structure, can be used to improve assignment of scaffolds to chromosomes. In addition, mRNA-sequence data can be used to economically acquire transcriptome information, which can be used for annotation. Some highly polymorphic and complex regions, for example MHC class I and immunoglobulin loci, will require extra effort to properly assemble and annotate. However, for the vast majority of genes, a modest investment in money, and a somewhat greater investment in time, can greatly improve assemblies and annotations sufficient to produce true, reference grade nonhuman primate genomes. Such resources can reasonably be expected to transform nonhuman primate research. PMID:24174438

  16. A semantic analysis of the annotations of the human genome.

    PubMed

    Khatri, Purvesh; Done, Bogdan; Rao, Archana; Done, Arina; Draghici, Sorin

    2005-08-15

    The correct interpretation of any biological experiment depends in an essential way on the accuracy and consistency of the existing annotation databases. Such databases are ubiquitous and used by all life scientists in most experiments. However, it is well known that such databases are incomplete and many annotations may also be incorrect. In this paper we describe a technique that can be used to analyze the semantic content of such annotation databases. Our approach is able to extract implicit semantic relationships between genes and functions. This ability allows us to discover novel functions for known genes. This approach is able to identify missing and inaccurate annotations in existing annotation databases, and thus help improve their accuracy. We used our technique to analyze the current annotations of the human genome. From this body of annotations, we were able to predict 212 additional gene-function assignments. A subsequent literature search found that 138 of these gene-functions assignments are supported by existing peer-reviewed papers. An additional 23 assignments have been confirmed in the meantime by the addition of the respective annotations in later releases of the Gene Ontology database. Overall, the 161 confirmed assignments represent 75.95% of the proposed gene-function assignments. Only one of our predictions (0.4%) was contradicted by the existing literature. We could not find any relevant articles for 50 of our predictions (23.58%). The method is independent of the organism and can be used to analyze and improve the quality of the data of any public or private annotation database. PMID:15955782

  17. Genome Annotation in a Community College Cell Biology Lab

    ERIC Educational Resources Information Center

    Beagley, C. Timothy

    2013-01-01

    The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning…

  18. A draft annotation and overview of the human genome

    PubMed Central

    Wright, Fred A; Lemon, William J; Zhao, Wei D; Sears, Russell; Zhuo, Degen; Wang, Jian-Ping; Yang, Hee-Yung; Baer, Troy; Stredney, Don; Spitzner, Joe; Stutz, Al; Krahe, Ralf; Yuan, Bo

    2001-01-01

    Background The recent draft assembly of the human genome provides a unified basis for describing genomic structure and function. The draft is sufficiently accurate to provide useful annotation, enabling direct observations of previously inferred biological phenomena. Results We report here a functionally annotated human gene index placed directly on the genome. The index is based on the integration of public transcript, protein, and mapping information, supplemented with computational prediction. We describe numerous global features of the genome and examine the relationship of various genetic maps with the assembly. In addition, initial sequence analysis reveals highly ordered chromosomal landscapes associated with paralogous gene clusters and distinct functional compartments. Finally, these annotation data were synthesized to produce observations of gene density and number that accord well with historical estimates. Such a global approach had previously been described only for chromosomes 21 and 22, which together account for 2.2% of the genome. Conclusions We estimate that the genome contains 65,000-75,000 transcriptional units, with exon sequences comprising 4%. The creation of a comprehensive gene index requires the synthesis of all available computational and experimental evidence. PMID:11516338

  19. Annotation of the Clostridium Acetobutylicum Genome

    SciTech Connect

    Daly, M. J.

    2004-06-09

    The genome sequence of the solvent producing bacterium Clostridium acetobutylicum ATCC824, has been determined by the shotgun approach. The genome consists of a 3.94 Mb chromosome and a 192 kb megaplasmid that contains the majority of genes responsible for solvent production. Comparison of C. acetobutylicum to Bacillus subtilis reveals significant local conservation of gene order, which has not been seen in comparisons of other genomes with similar, or, in some cases, closer, phylogenetic proximity. This conservation allows the prediction of many previously undetected operons in both bacteria.

  20. Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.

    PubMed

    Winsor, Geoffrey L; Griffiths, Emma J; Lo, Raymond; Dhillon, Bhavjinder K; Shay, Julie A; Brinkman, Fiona S L

    2016-01-01

    The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. PMID:26578582

  1. Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database

    PubMed Central

    Winsor, Geoffrey L.; Griffiths, Emma J.; Lo, Raymond; Dhillon, Bhavjinder K.; Shay, Julie A.; Brinkman, Fiona S. L.

    2016-01-01

    The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. PMID:26578582

  2. An Improved microRNA Annotation of the Canine Genome.

    PubMed

    Penso-Dolfin, Luca; Swofford, Ross; Johnson, Jeremy; Alföldi, Jessica; Lindblad-Toh, Kerstin; Swarbreck, David; Moxon, Simon; Di Palma, Federica

    2016-01-01

    The domestic dog, Canis familiaris, is a valuable model for studying human diseases. The publication of the latest Canine genome build and annotation, CanFam3.1 provides an opportunity to enhance our understanding of gene regulation across tissues in the dog model system. In this study, we used the latest dog genome assembly and small RNA sequencing data from 9 different dog tissues to predict novel miRNAs in the dog genome, as well as to annotate conserved miRNAs from the miRBase database that were missing from the current dog annotation. We used both miRCat and miRDeep2 algorithms to computationally predict miRNA loci. The resulting, putative hairpin sequences were analysed in order to discard false positives, based on predicted secondary structures and patterns of small RNA read alignments. Results were further divided into high and low confidence miRNAs, using the same criteria. We generated tissue specific expression profiles for the resulting set of 811 loci: 720 conserved miRNAs, (207 of which had not been previously annotated in the dog genome) and 91 novel miRNA loci. Comparative analyses revealed 8 putative homologues of some novel miRNA in ferret, and one in microbat. All miRNAs were also classified into the genic and intergenic categories, based on the Ensembl RefSeq gene annotation for CanFam3.1. This additionally allowed us to identify four previously undescribed MiRtrons among our total set of miRNAs. We additionally annotated piRNAs, using proTRAC on the same input data. We thus identified 263 putative clusters, most of which (211 clusters) were found to be expressed in testis. Our results represent an important improvement of the dog genome annotation, paving the way to further research on the evolution of gene regulation, as well as on the contribution of post-transcriptional regulation to pathological conditions. PMID:27119849

  3. An Improved microRNA Annotation of the Canine Genome

    PubMed Central

    Swofford, Ross; Johnson, Jeremy; Alföldi, Jessica; Lindblad-Toh, Kerstin; Swarbreck, David; Moxon, Simon; Di Palma, Federica

    2016-01-01

    The domestic dog, Canis familiaris, is a valuable model for studying human diseases. The publication of the latest Canine genome build and annotation, CanFam3.1 provides an opportunity to enhance our understanding of gene regulation across tissues in the dog model system. In this study, we used the latest dog genome assembly and small RNA sequencing data from 9 different dog tissues to predict novel miRNAs in the dog genome, as well as to annotate conserved miRNAs from the miRBase database that were missing from the current dog annotation. We used both miRCat and miRDeep2 algorithms to computationally predict miRNA loci. The resulting, putative hairpin sequences were analysed in order to discard false positives, based on predicted secondary structures and patterns of small RNA read alignments. Results were further divided into high and low confidence miRNAs, using the same criteria. We generated tissue specific expression profiles for the resulting set of 811 loci: 720 conserved miRNAs, (207 of which had not been previously annotated in the dog genome) and 91 novel miRNA loci. Comparative analyses revealed 8 putative homologues of some novel miRNA in ferret, and one in microbat. All miRNAs were also classified into the genic and intergenic categories, based on the Ensembl RefSeq gene annotation for CanFam3.1. This additionally allowed us to identify four previously undescribed MiRtrons among our total set of miRNAs. We additionally annotated piRNAs, using proTRAC on the same input data. We thus identified 263 putative clusters, most of which (211 clusters) were found to be expressed in testis. Our results represent an important improvement of the dog genome annotation, paving the way to further research on the evolution of gene regulation, as well as on the contribution of post-transcriptional regulation to pathological conditions. PMID:27119849

  4. MIPS: analysis and annotation of proteins from whole genomes.

    PubMed

    Mewes, H W; Amid, C; Arnold, R; Frishman, D; Güldener, U; Mannhaupt, G; Münsterkötter, M; Pagel, P; Strack, N; Stümpflen, V; Warfsmann, J; Ruepp, A

    2004-01-01

    The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis. The main focus of the work is directed toward the systematic organization of sequence-related attributes as gathered by a variety of algorithms, primary information from experimental data together with information compiled from the scientific literature. MIPS maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the database of complete cDNAs (German Human Genome Project, NGFN), the database of mammalian protein-protein interactions (MPPI), the database of FASTA homologies (SIMAP), and the interface for the fast retrieval of protein-associated information (QUIPOS). The Arabidopsis thaliana database, the rice database, the plant EST databases (MATDB, MOsDB, SPUTNIK), as well as the databases for the comprehensive set of genomes (PEDANT genomes) are described elsewhere in the 2003 and 2004 NAR database issues, respectively. All databases described, and the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de). PMID:14681354

  5. Aldo-keto reductase (AKR) superfamily: genomics and annotation.

    PubMed

    Mindnich, Rebekka D; Penning, Trevor M

    2009-07-01

    Aldo-keto reductases (AKRs) are phase I metabolising enzymes that catalyse the reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H)-dependent reduction of carbonyl groups to yield primary and secondary alcohols on a wide range of substrates, including aliphatic and aromatic aldehydes and ketones, ketoprostaglandins, ketosteroids and xenobiotics. In so doing they functionalise the carbonyl group for conjugation (phase II enzyme reactions). Although functionally diverse, AKRs form a protein superfamily based on their high sequence identity and common protein fold, the (alpha/beta) 8 -barrel structure. Well over 150 AKR enzymes, from diverse organisms, have been annotated so far and given systematic names according to a nomenclature that is based on multiple protein sequence alignment and degree of identity. Annotation of non-vertebrate AKRs at the National Center for Biotechnology Information or Vertebrate Genome Annotation (vega) database does not often include the systematic nomenclature name, so the most comprehensive overview of all annotated AKRs is found on the AKR website (http://www.med.upenn.edu/akr/). This site also hosts links to more detailed and specialised information (eg on crystal structures, gene expression and single nucleotide polymorphisms [SNPs]). The protein-based AKR nomenclature allows unambiguous identification of a given enzyme but does not reflect the wealth of genomic and transcriptomic variation that exists in the various databases. In this context, identification of putative new AKRs and their distinction from pseudogenes are challenging. This review provides a short summary of the characteristic features of AKR biochemistry and structure that have been reviewed in great detail elsewhere, and focuses mainly on nomenclature and database entries of human AKRs that so far have not been subject to systematic annotation. Recent developments in the annotation of SNP and transcript variance in AKRs are also summarised. PMID:19706366

  6. nGASP - the nematode genome annotation assessment project

    SciTech Connect

    Coghlan, A; Fiedler, T J; McKay, S J; Flicek, P; Harris, T W; Blasiar, D; Allen, J; Stein, L D

    2008-12-19

    While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second place. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy as reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs were the most challenging for gene-finders. While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C. elegans genome

  7. Genome Sequencing and Annotation of Mycobacterium tuberculosis PR08 strain.

    PubMed

    Jaafar, Mohammad Maaruf; Halim, Mohd Zakihalani A; Ismail, Mohamad Izwan; Shien, Lee Lian; Kek, Teh Lay; Fong, Ngeow Yun; Nor, Norazmi Mohd; Zainuddin, Zainul Fadziruddin; Hock, Tang Thean; Najimudin, Mohd Nazalan Mohd; Salleh, Mohd Zaki

    2016-03-01

    Mycobacterium tuberculosis is an acid fast bacterial species in the family Mycobacteriaceae and is the causative agent of most cases of tuberculosis. Here, we report the genomic features of Mycobacterium tuberculosis isolated from the cerebrospinal fluid (CSF) of a patient diagnosed with both pulmonary and extrapulmonary tuberculosis (TB). The isolated strain was identified as Mycobacterium tuberculosis PR08 (MTB PR08). Genomic DNA of the MTB PR08 strain was extracted and subjected to whole genome sequencing using MiSeq (Illumina, CA,USA). The draft genome size of MTB PR08 strain is 4,292,364 bp with a G + C content of 65.2%. This strain was annotated to have 4723 genes and 48 RNAs. This whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number CP010895. PMID:26981383

  8. GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

    PubMed Central

    Paila, Umadevi; Chapman, Brad A.; Kirchner, Rory; Quinlan, Aaron R.

    2013-01-01

    Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI's utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics. PMID:23874191

  9. Assembly, Annotation, and Analysis of Multiple Mycorrhizal Fungal Genomes

    SciTech Connect

    Initiative Consortium, Mycorrhizal Genomics; Kuo, Alan; Grigoriev, Igor; Kohler, Annegret; Martin, Francis

    2013-03-08

    Mycorrhizal fungi play critical roles in host plant health, soil community structure and chemistry, and carbon and nutrient cycling, all areas of intense interest to the US Dept. of Energy (DOE) Joint Genome Institute (JGI). To this end we are building on our earlier sequencing of the Laccaria bicolor genome by partnering with INRA-Nancy and the mycorrhizal research community in the MGI to sequence and analyze dozens of mycorrhizal genomes of all Basidiomycota and Ascomycota orders and multiple ecological types (ericoid, orchid, and ectomycorrhizal). JGI has developed and deployed high-throughput sequencing techniques, and Assembly, RNASeq, and Annotation Pipelines. In 2012 alone we sequenced, assembled, and annotated 12 draft or improved genomes of mycorrhizae, and predicted ~;;232831 genes and ~;;15011 multigene families, All of this data is publicly available on JGI MycoCosm (http://jgi.doe.gov/fungi/), which provides access to both the genome data and tools with which to analyze the data. Preliminary comparisons of the current total of 14 public mycorrhizal genomes suggest that 1) short secreted proteins potentially involved in symbiosis are more enriched in some orders than in others amongst the mycorrhizal Agaricomycetes, 2) there are wide ranges of numbers of genes involved in certain functional categories, such as signal transduction and post-translational modification, and 3) novel gene families are specific to some ecological types.

  10. Apollo: a sequence annotation editor

    PubMed Central

    Lewis, SE; Searle, SMJ; Harris, N; Gibson, M; Iyer, V; Richter, J; Wiel, C; Bayraktaroglu, L; Birney, E; Crosby, MA; Kaminker, JS; Matthews, BB; Prochnik, SE; Smith, CD; Tupy, JL; Rubin, GM; Misra, S; Mungall, CJ; Clamp, ME

    2002-01-01

    The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects. PMID:12537571

  11. SVA: software for annotating and visualizing sequenced human genomes

    PubMed Central

    Ge, Dongliang; Ruzzo, Elizabeth K.; Shianna, Kevin V.; He, Min; Pelak, Kimberly; Heinzen, Erin L.; Need, Anna C.; Cirulli, Elizabeth T.; Maia, Jessica M.; Dickson, Samuel P.; Zhu, Mingfu; Singh, Abanish; Allen, Andrew S.; Goldstein, David B.

    2011-01-01

    Summary: Here we present Sequence Variant Analyzer (SVA), a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. SVA also provides for flexible interaction with software implementing variant association tests allowing users to consider both the bioinformatic annotation of identified variants and the strength of their associations with studied traits. We illustrate the annotation features of SVA using two simple examples of sequenced genomes that harbor Mendelian mutations. Availability and implementation: Freely available on the web at http://www.svaproject.org. Contact: d.ge@duke.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21624899

  12. Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation

    PubMed Central

    Jackman, Shaun D.; Warren, René L.; Gibb, Ewan A.; Vandervalk, Benjamin P.; Mohamadi, Hamid; Chu, Justin; Raymond, Anthony; Pleasance, Stephen; Coope, Robin; Wildung, Mark R.; Ritland, Carol E.; Bousquet, Jean; Jones, Steven J. M.; Bohlmann, Joerg; Birol, Inanç

    2016-01-01

    The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, and reads of the organellar genomes were abundant in the data as each cell harbors hundreds of mitochondria and plastids. Hence, assembly of the 123-kb plastid and 5.9-Mb mitochondrial genomes were accomplished by analyzing data sets primarily representing low coverage of the nuclear genome. The assembled organellar genomes were annotated for their coding genes, ribosomal RNA, and transfer RNA. Transcript abundances of the mitochondrial genes were quantified in three developmental tissues and five mature tissues using data from RNA-seq experiments. C-to-U RNA editing was observed in the majority of mitochondrial genes, and in four genes, editing events were noted to modify ACG codons to create cryptic AUG start codons. The informatics methodology presented in this study should prove useful to assemble organellar genomes of other plant species using whole-genome shotgun sequencing data. PMID:26645680

  13. Design and implementation of a database for Brucella melitensis genome annotation.

    PubMed

    De Hertogh, Benoît; Lahlimi, Leïla; Lambert, Christophe; Letesson, Jean-Jacques; Depiereux, Eric

    2008-03-18

    The genome sequences of three Brucella biovars and of some species close to Brucella sp. have become available, leading to new relationship analysis. Moreover, the automatic genome annotation of the pathogenic bacteria Brucella melitensis has been manually corrected by a consortium of experts, leading to 899 modifications of start sites predictions among the 3198 open reading frames (ORFs) examined. This new annotation, coupled with the results of automatic annotation tools of the complete genome sequences of the B. melitensis genome (including BLASTs to 9 genomes close to Brucella), provides numerous data sets related to predicted functions, biochemical properties and phylogenic comparisons. To made these results available, alphaPAGe, a functional auto-updatable database of the corrected sequence genome of B. melitensis, has been built, using the entity-relationship (ER) approach and a multi-purpose database structure. A friendly graphical user interface has been designed, and users can carry out different kinds of information by three levels of queries: (1) the basic search use the classical keywords or sequence identifiers; (2) the original advanced search engine allows to combine (by using logical operators) numerous criteria: (a) keywords (textual comparison) related to the pCDS's function, family domains and cellular localization; (b) physico-chemical characteristics (numerical comparison) such as isoelectric point or molecular weight and structural criteria such as the nucleic length or the number of transmembrane helix (TMH); (c) similarity scores with Escherichia coli and 10 species phylogenetically close to B. melitensis; (3) complex queries can be performed by using a SQL field, which allows all queries respecting the database's structure. The database is publicly available through a Web server at the following url: http://www.fundp.ac.be/urbm/bioinfo/aPAGe. PMID:18160234

  14. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

    DOE PAGESBeta

    Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; et al

    2015-02-10

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offersmore » a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.« less

  15. The Annotator's Assistant: an expert system for direct submission of genetic sequence data.

    PubMed

    Bossinger, J A

    1988-03-01

    As DNA sequencing technology improves and more rapid techniques become routine in molecular biology labs, researchers need to expedite the incorporation of information into genetic sequence databases, such as GenBank, by directly submitting sequence data. The Annotator's Assistant is an expert system that runs on an IBM PC and helps the molecular biologist, who may have little knowledge of the structure or content of a GenBank entry, to construct a complete and valid sequence submission file. This expert system uses a simple molecular biology knowledge base and a selection of customized screen entry forms to guide the user through the entry and annotation of a sequence and its biological features. The system compiles information about the contributor, journal references, physical and functional characteristics of the nucleic acid, source organism and features, and checks it to eliminate incomplete answers and simple errors. Users supply input by answering direct and multiple-choice questions, selecting menu items and completing entry forms; on-line help is available. Users may also enter new or unusual information using generic forms. Several modules of the expert system were converted into Prolog programs and compiled, decreasing the running time significantly. The expert system rules and the data entry forms are easy to modify, update and customize for specific sequence classes. PMID:3382995

  16. The power of EST sequence data: Relation to Acyrthosiphon pisum genome annotation and functional genomics initiatives

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genes important to aphid biology, survival and reproduction were successfully identified by use of a genomics approach. We created and described the Sequencing, compilation, and annotation of the approxiamtely 525Mb nuclear genome of the pea aphid, Acyrthosiphon pisum, which represents an important ...

  17. The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations.

    PubMed

    Cherry, J Michael

    2015-12-01

    Genomic-scale assays result in data that provide information over the entire genome. Such base pair resolution data cannot be summarized easily except via a graphical viewer. A genome browser is a tool that displays genomic data and experimental results as horizontal tracks. Genome browsers allow searches for a chromosomal coordinate or a feature, such as a gene name, but they do not allow searches by function or upstream binding site. Entry into a genome browser requires that you identify the gene name or chromosomal coordinates for a region of interest. A track provides a representation for genomic results and is displayed as a row of data shown as line segments to indicate regions of the chromosome with a feature. Another type of track presents a graph or wiggle plot that indicates the processed signal intensity computed for a particular experiment or set of experiments. Wiggle plots are typical for genomic assays such as the various next-generation sequencing methods (e.g., chromatin immunoprecipitation [ChIP]-seq or RNA-seq), where it represents a peak of DNA binding, histone modification, or the mapping of an RNA sequence. Here we explore the browser that has been built into the Saccharomyces Genome Database (SGD). PMID:26631126

  18. xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud[OPEN

    PubMed Central

    Merchant, Nirav

    2016-01-01

    Genome-wide annotation of gene structure requires the integration of numerous computational steps. Currently, annotation is arguably best accomplished through collaboration of bioinformatics and domain experts, with broad community involvement. However, such a collaborative approach is not scalable at today’s pace of sequence generation. To address this problem, we developed the xGDBvm software, which uses an intuitive graphical user interface to access a number of common genome analysis and gene structure tools, preconfigured in a self-contained virtual machine image. Once their virtual machine instance is deployed through iPlant’s Atmosphere cloud services, users access the xGDBvm workflow via a unified Web interface to manage inputs, set program parameters, configure links to high-performance computing (HPC) resources, view and manage output, apply analysis and editing tools, or access contextual help. The xGDBvm workflow will mask the genome, compute spliced alignments from transcript and/or protein inputs (locally or on a remote HPC cluster), predict gene structures and gene structure quality, and display output in a public or private genome browser complete with accessory tools. Problematic gene predictions are flagged and can be reannotated using the integrated yrGATE annotation tool. xGDBvm can also be configured to append or replace existing data or load precomputed data. Multiple genomes can be annotated and displayed, and outputs can be archived for sharing or backup. xGDBvm can be adapted to a variety of use cases including de novo genome annotation, reannotation, comparison of different annotations, and training or teaching. PMID:27020957

  19. The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology

    PubMed Central

    Wang, Dapeng; Xia, Yan; Li, Xinna; Hou, Lixia; Yu, Jun

    2013-01-01

    Over the past 10 years, genomes of cultivated rice cultivars and their wild counterparts have been sequenced although most efforts are focused on genome assembly and annotation of two major cultivated rice (Oryza sativa L.) subspecies, 93-11 (indica) and Nipponbare (japonica). To integrate information from genome assemblies and annotations for better analysis and application, we now introduce a comparative rice genome database, the Rice Genome Knowledgebase (RGKbase, http://rgkbase.big.ac.cn/RGKbase/). RGKbase is built to have three major components: (i) integrated data curation for rice genomics and molecular biology, which includes genome sequence assemblies, transcriptomic and epigenomic data, genetic variations, quantitative trait loci (QTLs) and the relevant literature; (ii) User-friendly viewers, such as Gbrowse, GeneBrowse and Circos, for genome annotations and evolutionary dynamics and (iii) Bioinformatic tools for compositional and synteny analyses, gene family classifications, gene ontology terms and pathways and gene co-expression networks. RGKbase current includes data from five rice cultivars and species: Nipponbare (japonica), 93-11 (indica), PA64s (indica), the African rice (Oryza glaberrima) and a wild rice species (Oryza brachyantha). We are also constantly introducing new datasets from variety of public efforts, such as two recent releases—sequence data from ∼1000 rice varieties, which are mapped into the reference genome, yielding ample high-quality single-nucleotide polymorphisms and insertions–deletions. PMID:23193278

  20. MarinegenomicsDB: an integrated genome viewer for community-based annotation of genomes.

    PubMed

    Koyanagi, Ryo; Takeuchi, Takeshi; Hisata, Kanako; Gyoja, Fuki; Shoguchi, Eiichi; Satoh, Nori; Kawashima, Takeshi

    2013-10-01

    We constructed a web-based genome annotation platform, MarinegenomicsDB, to integrate genome data from various marine organisms including the pearl oyster Pinctada fucata and the coral Acropora digitifera. This newly developed viewer application provides open access to published data and a user-friendly environment for community-based manual gene annotation. Development on a flexible framework enables easy expansion of the website on demand. To date, more than 2000 genes have been annotated using this system. In the future, the website will be expanded to host a wider variety of data, more species, and different types of genome-wide analyses. The website is available at the following URL: http://marinegenomics.oist.jp. PMID:24125644

  1. A Human-Curated Annotation of the Candida albicans Genome

    PubMed Central

    Braun, Burkhard R; van het Hoog, Marco; d'Enfert, Christophe; Martchenko, Mikhail; Dungan, Jan; Kuo, Alan; Inglis, Diane O; Uhl, M. Andrew; Hogues, Hervé; Berriman, Matthew; Lorenz, Michael; Levitin, Anastasia; Oberholzer, Ursula; Bachewich, Catherine; Harcus, Doreen; Marcil, Anne; Dignard, Daniel; Iouk, Tatiana; Zito, Rosa; Frangeul, Lionel; Tekaia, Fredj; Rutherford, Kim; Wang, Edwin; Munro, Carol A; Bates, Steve; Gow, Neil A; Hoyer, Lois L; Köhler, Gerwald; Morschhäuser, Joachim; Newport, George; Znaidi, Sadri; Raymond, Martine; Turcotte, Bernard; Sherlock, Gavin; Costanzo, Maria; Ihmels, Jan; Berman, Judith; Sanglard, Dominique; Agabian, Nina; Mitchell, Aaron P; Johnson, Alexander D; Whiteway, Malcolm; Nantel, André

    2005-01-01

    Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications. PMID:16103911

  2. Re-Annotation Is an Essential Step in Systems Biology Modeling of Functional Genomics Data

    PubMed Central

    van den Berg, Bart H. J.; McCarthy, Fiona M.; Lamont, Susan J.; Burgess, Shane C.

    2010-01-01

    One motivation of systems biology research is to understand gene functions and interactions from functional genomics data such as that derived from microarrays. Up-to-date structural and functional annotations of genes are an essential foundation of systems biology modeling. We propose that the first essential step in any systems biology modeling of functional genomics data, especially for species with recently sequenced genomes, is gene structural and functional re-annotation. To demonstrate the impact of such re-annotation, we structurally and functionally re-annotated a microarray developed, and previously used, as a tool for disease research. We quantified the impact of this re-annotation on the array based on the total numbers of structural- and functional-annotations, the Gene Annotation Quality (GAQ) score, and canonical pathway coverage. We next quantified the impact of re-annotation on systems biology modeling using a previously published experiment that used this microarray. We show that re-annotation improves the quantity and quality of structural- and functional-annotations, allows a more comprehensive Gene Ontology based modeling, and improves pathway coverage for both the whole array and a differentially expressed mRNA subset. Our results also demonstrate that re-annotation can result in a different knowledge outcome derived from previous published research findings. We propose that, because of this, re-annotation should be considered to be an essential first step for deriving value from functional genomics data. PMID:20498845

  3. MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation.

    PubMed

    Lugli, Gabriele Andrea; Milani, Christian; Mancabelli, Leonardo; van Sinderen, Douwe; Ventura, Marco

    2016-04-01

    Genome annotation is one of the key actions that must be undertaken in order to decipher the genetic blueprint of organisms. Thus, a correct and reliable annotation is essential in rendering genomic data valuable. Here, we describe a bioinformatics pipeline based on freely available software programs coordinated by a multithreaded script named MEGAnnotator (Multithreaded Enhanced prokaryotic Genome Annotator). This pipeline allows the generation of multiple annotated formats fulfilling the NCBI guidelines for assembled microbial genome submission, based on DNA shotgun sequencing reads, and minimizes manual intervention, while also reducing waiting times between software program executions and improving final quality of both assembly and annotation outputs. MEGAnnotator provides an efficient way to pre-arrange the assembly and annotation work required to process NGS genome sequence data. The script improves the final quality of microbial genome annotation by reducing ambiguous annotations. Moreover, the MEGAnnotator platform allows the user to perform a partial annotation of pre-assembled genomes and includes an option to accomplish metagenomic data set assemblies. MEGAnnotator platform will be useful for microbiologists interested in genome analyses of bacteria as well as those investigating the complexity of microbial communities that do not possess the necessary skills to prepare their own bioinformatics pipeline. PMID:26936607

  4. The genomic CDS sandbox: An assessment among domain experts.

    PubMed

    Aziz, Ayesha; Kawamoto, Kensaku; Eilbeck, Karen; Williams, Marc S; Freimuth, Robert R; Hoffman, Mark A; Rasmussen, Luke V; Overby, Casey L; Shirts, Brian H; Hoffman, James M; Welch, Brandon M

    2016-04-01

    Genomics is a promising tool that is becoming more widely available to improve the care and treatment of individuals. While there is much assertion, genomics will most certainly require the use of clinical decision support (CDS) to be fully realized in the routine clinical setting. The National Human Genome Research Institute (NHGRI) of the National Institutes of Health recently convened an in-person, multi-day meeting on this topic. It was widely recognized that there is a need to promote the innovation and development of resources for genomic CDS such as a CDS sandbox. The purpose of this study was to evaluate a proposed approach for such a genomic CDS sandbox among domain experts and potential users. Survey results indicate a significant interest and desire for a genomic CDS sandbox environment among domain experts. These results will be used to guide the development of a genomic CDS sandbox. PMID:26778834

  5. The Genomic CDS Sandbox: An Assessment Among Domain Experts

    PubMed Central

    Aziz, Ayesha; Kawamoto, Kensaku; Eilbeck, Karen; Williams, Marc S.; Freimuth, Robert R.; Hoffman, Mark A.; Rasmussen, Luke V.; Overby, Casey L.; Shirts, Brian H.; Hoffman, James M.; Welch, Brandon M.

    2016-01-01

    Genomics is a promising tool that is becoming more widely available to improve the care and treatment of individuals. While there is much assertion, genomics will most certainly require the use of clinical decision support (CDS) to be fully realized in the routine clinical setting. The National Human Genome Research Institute (NHGRI) of the National Institutes of Health recently convened an in-person, multi-day meeting on this topic. It was widely recognized that there is a need to promote the innovation and development of resources for genomic CDS such as a CDS sandbox. The purpose of this study was to evaluate a proposed approach for such a genomic CDS sandbox among domain experts and potential users. Survey results indicate a significant interest and desire for a genomic CDS sandbox environment among domain experts. These results will be used to guide the development of a genomic CDS sandbox. PMID:26778834

  6. AGeS: A Software System for Microbial Genome Sequence Annotation

    PubMed Central

    Kumar, Kamal; Desai, Valmik; Cheng, Li; Khitrov, Maxim; Grover, Deepak; Satya, Ravi Vijaya; Yu, Chenggang; Zavaljevski, Nela; Reifman, Jaques

    2011-01-01

    Background The annotation of genomes from next-generation sequencing platforms needs to be rapid, high-throughput, and fully integrated and automated. Although a few Web-based annotation services have recently become available, they may not be the best solution for researchers that need to annotate a large number of genomes, possibly including proprietary data, and store them locally for further analysis. To address this need, we developed a standalone software application, the Annotation of microbial Genome Sequences (AGeS) system, which incorporates publicly available and in-house-developed bioinformatics tools and databases, many of which are parallelized for high-throughput performance. Methodology The AGeS system supports three main capabilities. The first is the storage of input contig sequences and the resulting annotation data in a central, customized database. The second is the annotation of microbial genomes using an integrated software pipeline, which first analyzes contigs from high-throughput sequencing by locating genomic regions that code for proteins, RNA, and other genomic elements through the Do-It-Yourself Annotation (DIYA) framework. The identified protein-coding regions are then functionally annotated using the in-house-developed Pipeline for Protein Annotation (PIPA). The third capability is the visualization of annotated sequences using GBrowse. To date, we have implemented these capabilities for bacterial genomes. AGeS was evaluated by comparing its genome annotations with those provided by three other methods. Our results indicate that the software tools integrated into AGeS provide annotations that are in general agreement with those provided by the compared methods. This is demonstrated by a >94% overlap in the number of identified genes, a significant number of identical annotated features, and a >90% agreement in enzyme function predictions. PMID:21408217

  7. The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms.

    PubMed

    McGuffin, Liam J; Street, Stefano A; Bryson, Kevin; Sørensen, Søren-Aksel; Jones, David T

    2004-01-01

    Currently, the Genomic Threading Database (GTD) contains structural assignments for the proteins encoded within the genomes of nine eukaryotes and 101 prokaryotes. Structural annotations are carried out using a modified version of GenTHREADER, a reliable fold recognition method. The Gen THREADER annotation jobs are distributed across multiple clusters of processors using grid technology and the predictions are deposited in a relational database accessible via a web interface at http://bioinf.cs.ucl.ac.uk/GTD. Using this system, up to 84% of proteins encoded within a genome can be confidently assigned to known folds with 72% of the residues aligned. On average in the GTD, 64% of proteins encoded within a genome are confidently assigned to known folds and 58% of the residues are aligned to structures. PMID:14681393

  8. The Effect of Human Genome Annotation Complexity on RNA-Seq Gene Expression Quantification

    PubMed Central

    Wu, Po-Yen; Phan, John H.; Wang, May D.

    2016-01-01

    Next-generation sequencing (NGS) has brought human genomic research to an unprecedented era. RNA-Seq is a branch of NGS that can be used to quantify gene expression and depends on accurate annotation of the human genome (i.e., the definition of genes and all of their variants or isoforms). Multiple annotations of the human genome exist with varying complexity. However, it is not clear how the choice of genome annotation influences RNA-Seq gene expression quantification. We assess the effect of different genome annotations in terms of (1) mapping quality, (2) quantification variation, (3) quantification accuracy (i.e., by comparing to qRT-PCR data), and (4) the concordance of detecting differentially expressed genes. External validation with qRT-PCR suggests that more complex genome annotations result in higher quantification variation.

  9. MaGe: a microbial genome annotation system supported by synteny results.

    PubMed

    Vallenet, David; Labarre, Laurent; Rouy, Zoé; Barbe, Valérie; Bocs, Stéphanie; Cruveiller, Stéphane; Lajus, Aurélie; Pascal, Géraldine; Scarpelli, Claude; Médigue, Claudine

    2006-01-01

    Magnifying Genomes (MaGe) is a microbial genome annotation system based on a relational database containing information on bacterial genomes, as well as a web interface to achieve genome annotation projects. Our system allows one to initiate the annotation of a genome at the early stage of the finishing phase. MaGe's main features are (i) integration of annotation data from bacterial genomes enhanced by a gene coding re-annotation process using accurate gene models, (ii) integration of results obtained with a wide range of bioinformatics methods, among which exploration of gene context by searching for conserved synteny and reconstruction of metabolic pathways, (iii) an advanced web interface allowing multiple users to refine the automatic assignment of gene product functions. MaGe is also linked to numerous well-known biological databases and systems. Our system has been thoroughly tested during the annotation of complete bacterial genomes (Acinetobacter baylyi ADP1, Pseudoalteromonas haloplanktis, Frankia alni) and is currently used in the context of several new microbial genome annotation projects. In addition, MaGe allows for annotation curation and exploration of already published genomes from various genera (e.g. Yersinia, Bacillus and Neisseria). MaGe can be accessed at http://www.genoscope.cns.fr/agc/mage. PMID:16407324

  10. MaGe: a microbial genome annotation system supported by synteny results

    PubMed Central

    Vallenet, David; Labarre, Laurent; Rouy, Zoé; Barbe, Valérie; Bocs, Stéphanie; Cruveiller, Stéphane; Lajus, Aurélie; Pascal, Géraldine; Scarpelli, Claude; Médigue, Claudine

    2006-01-01

    Magnifying Genomes (MaGe) is a microbial genome annotation system based on a relational database containing information on bacterial genomes, as well as a web interface to achieve genome annotation projects. Our system allows one to initiate the annotation of a genome at the early stage of the finishing phase. MaGe's main features are (i) integration of annotation data from bacterial genomes enhanced by a gene coding re-annotation process using accurate gene models, (ii) integration of results obtained with a wide range of bioinformatics methods, among which exploration of gene context by searching for conserved synteny and reconstruction of metabolic pathways, (iii) an advanced web interface allowing multiple users to refine the automatic assignment of gene product functions. MaGe is also linked to numerous well-known biological databases and systems. Our system has been thoroughly tested during the annotation of complete bacterial genomes (Acinetobacter baylyi ADP1, Pseudoalteromonas haloplanktis, Frankia alni) and is currently used in the context of several new microbial genome annotation projects. In addition, MaGe allows for annotation curation and exploration of already published genomes from various genera (e.g. Yersinia, Bacillus and Neisseria). MaGe can be accessed at . PMID:16407324

  11. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An annotation-based, genome-wide SNP discovery pipeline is reported using NGS data for large and complex genomes without a reference genome sequence. Roche 454 shotgun reads with low genome coverage of one genotype are annotated in order to distinguish single-copy sequences and repeat junctions fr...

  12. Coordinated international action to accelerate genome-to-phenome with FAANG, The Functional Annotation of Animal Genomes project

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We describe the organization of a nascent international effort - the "Functional Annotation of ANimal Genomes" project - whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species....

  13. Biological database of images and genomes: tools for community annotations linking image and genomic information.

    PubMed

    Oberlin, Andrew T; Jurkovic, Dominika A; Balish, Mitchell F; Friedberg, Iddo

    2013-01-01

    Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype-genotype connection linking the two types of data is lagging behind. While there are many types of software that enable the manipulation and analysis of image data and genomic data as separate entities, there is no framework established for linking the two. We present a generic set of software tools, BioDIG, that allows linking of image data to genomic data. BioDIG tools can be applied to a wide range of research problems that require linking images to genomes. BioDIG features the following: rapid construction of web-based workbenches, community-based annotation, user management and web services. By using BioDIG to create websites, researchers and curators can rapidly annotate a large number of images with genomic information. Here we present the BioDIG software tools that include an image module, a genome module and a user management module. We also introduce a BioDIG-based website, MyDIG, which is being used to annotate images of mycoplasmas. PMID:23550062

  14. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4).

    PubMed

    Huntemann, Marcel; Ivanova, Natalia N; Mavromatis, Konstantinos; Tripp, H James; Paez-Espino, David; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A; Pati, Amrita; Nielsen, Torben; Markowitz, Victor M; Kyrpides, Nikos C

    2015-01-01

    The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. Structural annotation is followed by assignment of protein product names and functions. PMID:26512311

  15. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

    SciTech Connect

    Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; Tripp, H. James; Paez-Espino, David; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A.; Pati, Amrita; Nielsen, Torben; Markowitz, Victor M.; Kyrpides, Nikos C.

    2015-10-26

    The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. In conclusion, structural annotation is followed by assignment of protein product names and functions.

  16. An integrated computational pipeline and database to support whole-genome sequence annotation

    PubMed Central

    Mungall, CJ; Misra, S; Berman, BP; Carlson, J; Frise, E; Harris, N; Marshall, B; Shu, S; Kaminker, JS; Prochnik, SE; Smith, CD; Smith, E; Tupy, JL; Wiel, C; Rubin, GM; Lewis, SE

    2002-01-01

    We describe here our experience in annotating the Drosophila melanogaster genome sequence, in the course of which we developed several new open-source software tools and a database schema to support large-scale genome annotation. We have developed these into an integrated and reusable software system for whole-genome annotation. The key contributions to overall annotation quality are the marshalling of high-quality sequences for alignments and the design of a system with an adaptable and expandable flexible architecture. PMID:12537570

  17. MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline

    PubMed Central

    Iwasaki, Wataru; Fukunaga, Tsukasa; Isagozawa, Ryota; Yamada, Koichiro; Maeda, Yasunobu; Satoh, Takashi P.; Sado, Tetsuya; Mabuchi, Kohji; Takeshima, Hirohiko; Miya, Masaki; Nishida, Mutsumi

    2013-01-01

    Mitofish is a database of fish mitochondrial genomes (mitogenomes) that includes powerful and precise de novo annotations for mitogenome sequences. Fish occupy an important position in the evolution of vertebrates and the ecology of the hydrosphere, and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new fish species. The importance of a mitogenomic database continues to grow at a rapid pace as massive amounts of mitogenomic data are generated with the advent of new sequencing technologies. A severe bottleneck seems likely to occur with regard to mitogenome annotation because of the overwhelming pace of data accumulation and the intrinsic difficulties in annotating sequences with degenerating transfer RNA structures, divergent start/stop codons of the coding elements, and the overlapping of adjacent elements. To ease this data backlog, we developed an annotation pipeline named MitoAnnotator. MitoAnnotator automatically annotates a fish mitogenome with a high degree of accuracy in approximately 5 min; thus, it is readily applicable to data sets of dozens of sequences. MitoFish also contains re-annotations of previously sequenced fish mitogenomes, enabling researchers to refer to them when they find annotations that are likely to be erroneous or while conducting comparative mitogenomic analyses. For users who need more information on the taxonomy, habitats, phenotypes, or life cycles of fish, MitoFish provides links to related databases. MitoFish and MitoAnnotator are freely available at http://mitofish.aori.u-tokyo.ac.jp/ (last accessed August 28, 2013); all of the data can be batch downloaded, and the annotation pipeline can be used via a web interface. PMID:23955518

  18. MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline.

    PubMed

    Iwasaki, Wataru; Fukunaga, Tsukasa; Isagozawa, Ryota; Yamada, Koichiro; Maeda, Yasunobu; Satoh, Takashi P; Sado, Tetsuya; Mabuchi, Kohji; Takeshima, Hirohiko; Miya, Masaki; Nishida, Mutsumi

    2013-11-01

    Mitofish is a database of fish mitochondrial genomes (mitogenomes) that includes powerful and precise de novo annotations for mitogenome sequences. Fish occupy an important position in the evolution of vertebrates and the ecology of the hydrosphere, and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new fish species. The importance of a mitogenomic database continues to grow at a rapid pace as massive amounts of mitogenomic data are generated with the advent of new sequencing technologies. A severe bottleneck seems likely to occur with regard to mitogenome annotation because of the overwhelming pace of data accumulation and the intrinsic difficulties in annotating sequences with degenerating transfer RNA structures, divergent start/stop codons of the coding elements, and the overlapping of adjacent elements. To ease this data backlog, we developed an annotation pipeline named MitoAnnotator. MitoAnnotator automatically annotates a fish mitogenome with a high degree of accuracy in approximately 5 min; thus, it is readily applicable to data sets of dozens of sequences. MitoFish also contains re-annotations of previously sequenced fish mitogenomes, enabling researchers to refer to them when they find annotations that are likely to be erroneous or while conducting comparative mitogenomic analyses. For users who need more information on the taxonomy, habitats, phenotypes, or life cycles of fish, MitoFish provides links to related databases. MitoFish and MitoAnnotator are freely available at http://mitofish.aori.u-tokyo.ac.jp/ (last accessed August 28, 2013); all of the data can be batch downloaded, and the annotation pipeline can be used via a web interface. PMID:23955518

  19. The discrepancies in the results of bioinformatics tools for genomic structural annotation

    NASA Astrophysics Data System (ADS)

    Pawełkowicz, Magdalena; Nowak, Robert; Osipowski, Paweł; Rymuszka, Jacek; Świerkula, Katarzyna; Wojcieszek, Michał; Przybecki, Zbigniew

    2014-11-01

    A major focus of sequencing project is to identify genes in genomes. However it is necessary to define the variety of genes and the criteria for identifying them. In this work we present discrepancies and dependencies from the application of different bioinformatic programs for structural annotation performed on the cucumber data set from Polish Consortium of Cucumber Genome Sequencing. We use Fgenesh, GenScan and GeneMark to automated structural annotation, the results have been compared to reference annotation.

  20. Manual curation is not sufficient for annotation of genomic databases

    PubMed Central

    Baumgartner, William A.; Cohen, K. Bretonnel; Fox, Lynne M.; Acquaah-Mensah, George; Hunter, Lawrence

    2008-01-01

    Motivation Knowledge base construction has been an area of intense activity and great importance in the growth of computational biology. However, there is little or no history of work on the subject of evaluation of knowledge bases, either with respect to their contents or with respect to the processes by which they are constructed. This article proposes the application of a metric from software engineering known as the found/fixed graph to the problem of evaluating the processes by which genomic knowledge bases are built, as well as the completeness of their contents. Results Well-understood patterns of change in the found/fixed graph are found to occur in two large publicly available knowledge bases. These patterns suggest that the current manual curation processes will take far too long to complete the annotations of even just the most important model organisms, and that at their current rate of production, they will never be sufficient for completing the annotation of all currently available proteomes. Contact larry.hunter@uchsc.edu PMID:17646325

  1. VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data

    SciTech Connect

    Peterson, Elena S.; McCue, Lee Ann; Rutledge, Alexandra C.; Jensen, Jeffrey L.; Walker, Julia; Kobold, Mark A.; Webb, Samantha R.; Payne, Samuel H.; Ansong, Charles; Adkins, Joshua N.; Cannon, William R.; Webb-Robertson, Bobbie-Jo M.

    2012-04-25

    Visual Exploration and Statistics to Promote Annotation (VESPA) is an interactive visual analysis software tool that facilitates the discovery of structural mis-annotations in prokaryotic genomes. VESPA integrates high-throughput peptide-centric proteomics data and oligo-centric or RNA-Seq transcriptomics data into a genomic context. The data may be interrogated via visual analysis across multiple levels of genomic resolution, linked searches, exports and interaction with BLAST to rapidly identify location of interest within the genome and evaluate potential mis-annotations.

  2. Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach

    PubMed Central

    2013-01-01

    Background Accurate bacterial genome annotations provide a framework to understanding cellular functions, behavior and pathogenicity and are essential for metabolic engineering. Annotations based only on in silico predictions are inaccurate, particularly for large, high G + C content genomes due to the lack of similarities in gene length and gene organization to model organisms. Results Here we describe a 2D systems biology driven re-annotation of the Saccharopolyspora erythraea genome using proteogenomics, a genome-scale metabolic reconstruction, RNA-sequencing and small-RNA-sequencing. We observed transcription of more than 300 intergenic regions, detected 59 peptides in intergenic regions, confirmed 164 open reading frames previously annotated as hypothetical proteins and reassigned function to open reading frames using the genome-scale metabolic reconstruction. Finally, we present a novel way of mapping ribosomal binding sites across the genome by sequencing small RNAs. Conclusions The work presented here describes a novel framework for annotation of the Saccharopolyspora erythraea genome. Based on experimental observations, the 2D annotation framework greatly reduces errors that are commonly made when annotating large-high G + C content genomes using computational prediction algorithms. PMID:24118942

  3. MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes

    PubMed Central

    Cantarel, Brandi L.; Korf, Ian; Robb, Sofia M.C.; Parra, Genis; Ross, Eric; Moore, Barry; Holt, Carson; Sánchez Alvarado, Alejandro; Yandell, Mark

    2008-01-01

    We have developed a portable and easily configurable genome annotation pipeline called MAKER. Its purpose is to allow investigators to independently annotate eukaryotic genomes and create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions, and automatically synthesizes these data into gene annotations having evidence-based quality indices. MAKER is also easily trainable: Outputs of preliminary runs are used to automatically retrain its gene-prediction algorithm, producing higher-quality gene-models on subsequent runs. MAKER’s inputs are minimal, and its outputs can be used to create a GMOD database. Its outputs can also be viewed in the Apollo Genome browser; this feature of MAKER provides an easy means to annotate, view, and edit individual contigs and BACs without the overhead of a database. As proof of principle, we have used MAKER to annotate the genome of the planarian Schmidtea mediterranea and to create a new genome database, SmedGD. We have also compared MAKER’s performance to other published annotation pipelines. Our results demonstrate that MAKER provides a simple and effective means to convert a genome sequence into a community-accessible genome database. MAKER should prove especially useful for emerging model organism genome projects for which extensive bioinformatics resources may not be readily available. PMID:18025269

  4. Australian sea-floor survey data, with images and expert annotations

    PubMed Central

    Bewley, Michael; Friedman, Ariell; Ferrari, Renata; Hill, Nicole; Hovey, Renae; Barrett, Neville; Pizarro, Oscar; Figueira, Will; Meyer, Lisa; Babcock, Russ; Bellchambers, Lynda; Byrne, Maria; Williams, Stefan B.

    2015-01-01

    This Australian benthic data set (BENTHOZ-2015) consists of an expert-annotated set of georeferenced benthic images and associated sensor data, captured by an autonomous underwater vehicle (AUV) around Australia. This type of data is of interest to marine scientists studying benthic habitats and organisms. AUVs collect georeferenced images over an area with consistent illumination and altitude, and make it possible to generate broad scale, photo-realistic 3D maps. Marine scientists then typically spend several minutes on each of thousands of images, labeling substratum type and biota at a subset of points. Labels from four Australian research groups were combined using the CATAMI classification scheme, a hierarchical classification scheme based on taxonomy and morphology for scoring marine imagery. This data set consists of 407,968 expert labeled points from around the Australian coast, with associated images, geolocation and other sensor data. The robotic surveys that collected this data form part of Australia's Integrated Marine Observing System (IMOS) ongoing benthic monitoring program. There is reuse potential in marine science, robotics, and computer vision research. PMID:26528396

  5. Australian sea-floor survey data, with images and expert annotations.

    PubMed

    Bewley, Michael; Friedman, Ariell; Ferrari, Renata; Hill, Nicole; Hovey, Renae; Barrett, Neville; Pizarro, Oscar; Figueira, Will; Meyer, Lisa; Babcock, Russ; Bellchambers, Lynda; Byrne, Maria; Williams, Stefan B

    2015-01-01

    This Australian benthic data set (BENTHOZ-2015) consists of an expert-annotated set of georeferenced benthic images and associated sensor data, captured by an autonomous underwater vehicle (AUV) around Australia. This type of data is of interest to marine scientists studying benthic habitats and organisms. AUVs collect georeferenced images over an area with consistent illumination and altitude, and make it possible to generate broad scale, photo-realistic 3D maps. Marine scientists then typically spend several minutes on each of thousands of images, labeling substratum type and biota at a subset of points. Labels from four Australian research groups were combined using the CATAMI classification scheme, a hierarchical classification scheme based on taxonomy and morphology for scoring marine imagery. This data set consists of 407,968 expert labeled points from around the Australian coast, with associated images, geolocation and other sensor data. The robotic surveys that collected this data form part of Australia's Integrated Marine Observing System (IMOS) ongoing benthic monitoring program. There is reuse potential in marine science, robotics, and computer vision research. PMID:26528396

  6. Genomic Test Results and the Courtroom: The Roles of Experts and Expert Testimony.

    PubMed

    Ramos, Edward; Callier, Shawneequa L; Swann, Peter B; Harvey, Hosea H

    2016-03-01

    The rapid advancement from single-gene testing to whole genome sequencing has significantly broadened the type and amount of information available to researchers, physicians, patients, and the public in general. Much debate has ensued about whether genomic test results should be reported to research participants, patients and consumers, and at what stage we can be sure that existing evidence justifies their use in clinical settings. Courts and judges evaluating the utility of these results will not be immune to this uncertainty. As scholars increasingly explore the duty of care standards related to reporting genomic test results, it is timely to provide a framework for understanding how uncertainty about genetic and genomic tests influences evidentiary considerations in the court room. Here, we explore the subtleties and nuances of interpreting genetic data in an environment of substantial discord related to the value that individuals should place on genetic and genomic tests. In conjunction, we discuss the roles courts should play in qualifying experts, expert testimony, and genetic and genomic tests given the intricate and complex nature of genetic and genomic information. PMID:27256136

  7. Improvement of barley genome annotations by deciphering the Haruna Nijo genome

    PubMed Central

    Sato, Kazuhiro; Tanaka, Tsuyoshi; Shigenobu, Shuji; Motoi, Yuka; Wu, Jianzhong; Itoh, Takeshi

    2016-01-01

    Full-length (FL) cDNA sequences provide the most reliable evidence for the presence of genes in genomes. In this report, detailed gene structures of barley, whole genome shotgun (WGS) and additional transcript data of the cultivar Haruna Nijo were quality controlled and compared with the published Morex genome information. Haruna Nijo scaffolds have longer total sequence length with much higher N50 and fewer sequences than those in Morex WGS contigs. The longer Haruna Nijo scaffolds provided efficient FLcDNA mapping, resulting in high coverage and detection of the transcription start sites. In combination with FLcDNAs and RNA-Seq data from four different tissue samples of Haruna Nijo, we identified 51,249 gene models on 30,606 loci. Overall sequence similarity between Haruna Nijo and Morex genome was 95.99%, while that of exon regions was higher (99.71%). These sequence and annotation data of Haruna Nijo are combined with Morex genome data and released from a genome browser. The genome sequence of Haruna Nijo may provide detailed gene structures in addition to the current Morex barley genome information. PMID:26622062

  8. Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.

    PubMed

    Ito, Yuichi; Arikawa, Kohji; Antonio, Baltazar A; Ohta, Isamu; Naito, Shinji; Mukai, Yoshiyuki; Shimano, Atsuko; Masukawa, Masatoshi; Shibata, Michie; Yamamoto, Mayu; Ito, Yukiyo; Yokoyama, Junri; Sakai, Yasumichi; Sakata, Katsumi; Nagamura, Yoshiaki; Namiki, Nobukazu; Matsumoto, Takashi; Higo, Kenichi; Sasaki, Takuji

    2005-01-01

    A contig-oriented database for annotation of the rice genome has been constructed to facilitate map-based rice genomics. The Rice Annotation Database has the following functional features: (i) extensive effort of manual annotations of P1-derived artificial chromosome/bacterial artificial chromosome clones can be merged at chromosome and contig-level; (ii) concise visualization of the annotation information such as the predicted genes, results of various prediction programs (RiceHMM, Genscan, Genscan+, Fgenesh, GeneMark, etc.), homology to expressed sequence tag, full-length cDNA and protein; (iii) user-friendly clone / gene query system; (iv) download functions for nucleotide, amino acid and coding sequences; (v) analysis of various features of the genome (GC-content, average value, etc.); and (vi) genome-wide homology search (BLAST) of contig- and chromosome-level genome sequence to allow comparative analysis with the genome sequence of other organisms. As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results including 30 000 manually curated genes. The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome. The database can be accessed at http://rad.dna.affrc.go.jp/. PMID:15608281

  9. Toward a standard in structural genome annotation for prokaryotes

    SciTech Connect

    Tripp, H. James; Sutton, Granger; White, Owen; Wortman, Jennifer; Pati, Amrita; Mikhailova, Natalia; Ovchinnikova, Galina; Payne, Samuel H.; Kyrpides, Nikos C.; Ivanova, Natalia

    2015-07-25

    In an effort to identify the best practice for finding genes in prokaryotic genomes and propose it as a standard for automated annotation pipelines, we collected 1,004,576 peptides from various publicly available resources, and these were used as a basis to evaluate various gene-calling methods. The peptides came from 45 bacterial replicons with an average GC content from 31 % to 74 %, biased toward higher GC content genomes. Automated, manual, and semi-manual methods were used to tally errors in three widely used gene calling methods, as evidenced by peptides mapped outside the boundaries of called genes. We found that the consensus set of identical genes predicted by the three methods constitutes only about 70 % of the genes predicted by each individual method (with start and stop required to coincide). Peptide data was useful for evaluating some of the differences between gene callers, but not reliable enough to make the results conclusive, due to limitations inherent in any proteogenomic study. A single, unambiguous, unanimous best practice did not emerge from this analysis, since the available proteomics data were not adequate to provide an objective measurement of differences in the accuracy between these methods. However, as a result of this study, software, reference data, and procedures have been better matched among participants, representing a step toward a much-needed standard. In the absence of sufficient amount of experimental data to achieve a universal standard, our recommendation is that any of these methods can be used by the community, as long as a single method is employed across all datasets to be compared.

  10. Toward a standard in structural genome annotation for prokaryotes

    DOE PAGESBeta

    Tripp, H. James; Sutton, Granger; White, Owen; Wortman, Jennifer; Pati, Amrita; Mikhailova, Natalia; Ovchinnikova, Galina; Payne, Samuel H.; Kyrpides, Nikos C.; Ivanova, Natalia

    2015-07-25

    In an effort to identify the best practice for finding genes in prokaryotic genomes and propose it as a standard for automated annotation pipelines, we collected 1,004,576 peptides from various publicly available resources, and these were used as a basis to evaluate various gene-calling methods. The peptides came from 45 bacterial replicons with an average GC content from 31 % to 74 %, biased toward higher GC content genomes. Automated, manual, and semi-manual methods were used to tally errors in three widely used gene calling methods, as evidenced by peptides mapped outside the boundaries of called genes. We found thatmore » the consensus set of identical genes predicted by the three methods constitutes only about 70 % of the genes predicted by each individual method (with start and stop required to coincide). Peptide data was useful for evaluating some of the differences between gene callers, but not reliable enough to make the results conclusive, due to limitations inherent in any proteogenomic study. A single, unambiguous, unanimous best practice did not emerge from this analysis, since the available proteomics data were not adequate to provide an objective measurement of differences in the accuracy between these methods. However, as a result of this study, software, reference data, and procedures have been better matched among participants, representing a step toward a much-needed standard. In the absence of sufficient amount of experimental data to achieve a universal standard, our recommendation is that any of these methods can be used by the community, as long as a single method is employed across all datasets to be compared.« less

  11. Proteogenomics: the needs and roles to be filled by proteomics in genome annotation

    SciTech Connect

    Ansong, Charles; Purvine, Samuel O.; Adkins, Joshua N.; Lipton, Mary S.; Smith, Richard D.

    2008-01-01

    While genome sequencing efforts reveal the basic building blocks of life, a genome sequence alone is insufficient for elucidating biological function. Genome annotation – the process of identifying genes and assigning function to each gene in a genome sequence – provides the means to elucidate biological function from sequence. Current state-of-the-art high throughput genome annotation uses a combination of comparative (sequence similarity data) and non-comparative (ab initio gene prediction algorithms) methods to identify open reading frames in genome sequences. Because approaches used to validate the presence of these open reading frames are typically based on the information derived from the annotated genomes, they cannot independently and unequivocally determine whether a predicted open reading frame is translated into a protein. With the ability to directly measure peptides arising from expressed proteins, high throughput liquid chromatography-tandem mass spectrometry-based proteomics, approaches can be used to verify coding regions of a genomic sequence. Here, we highlight several ways in which high throughput tandem mass spectrometry-based proteomics can improve the quality of genome annotations and suggest that it could be efficiently applied during the initial gene calling process so that the improvements are propagated through the subsequent functional annotation process.

  12. BG7: a new approach for bacterial genome annotation designed for next generation sequencing data.

    PubMed

    Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Pareja, Eduardo; Tobes, Raquel

    2012-01-01

    BG7 is a new system for de novo bacterial, archaeal and viral genome annotation based on a new approach specifically designed for annotating genomes sequenced with next generation sequencing technologies. The system is versatile and able to annotate genes even in the step of preliminary assembly of the genome. It is especially efficient detecting unexpected genes horizontally acquired from bacterial or archaeal distant genomes, phages, plasmids, and mobile elements. From the initial phases of the gene annotation process, BG7 exploits the massive availability of annotated protein sequences in databases. BG7 predicts ORFs and infers their function based on protein similarity with a wide set of reference proteins, integrating ORF prediction and functional annotation phases in just one step. BG7 is especially tolerant to sequencing errors in start and stop codons, to frameshifts, and to assembly or scaffolding errors. The system is also tolerant to the high level of gene fragmentation which is frequently found in not fully assembled genomes. BG7 current version - which is developed in Java, takes advantage of Amazon Web Services (AWS) cloud computing features, but it can also be run locally in any operating system. BG7 is a fast, automated and scalable system that can cope with the challenge of analyzing the huge amount of genomes that are being sequenced with NGS technologies. Its capabilities and efficiency were demonstrated in the 2011 EHEC Germany outbreak in which BG7 was used to get the first annotations right the next day after the first entero-hemorrhagic E. coli genome sequences were made publicly available. The suitability of BG7 for genome annotation has been proved for Illumina, 454, Ion Torrent, and PacBio sequencing technologies. Besides, thanks to its plasticity, our system could be very easily adapted to work with new technologies in the future. PMID:23185310

  13. Genomic analyses with biofilter 2.0: knowledge driven filtering, annotation, and model development

    PubMed Central

    2013-01-01

    Background The ever-growing wealth of biological information available through multiple comprehensive database repositories can be leveraged for advanced analysis of data. We have now extensively revised and updated the multi-purpose software tool Biofilter that allows researchers to annotate and/or filter data as well as generate gene-gene interaction models based on existing biological knowledge. Biofilter now has the Library of Knowledge Integration (LOKI), for accessing and integrating existing comprehensive database information, including more flexibility for how ambiguity of gene identifiers are handled. We have also updated the way importance scores for interaction models are generated. In addition, Biofilter 2.0 now works with a range of types and formats of data, including single nucleotide polymorphism (SNP) identifiers, rare variant identifiers, base pair positions, gene symbols, genetic regions, and copy number variant (CNV) location information. Results Biofilter provides a convenient single interface for accessing multiple publicly available human genetic data sources that have been compiled in the supporting database of LOKI. Information within LOKI includes genomic locations of SNPs and genes, as well as known relationships among genes and proteins such as interaction pairs, pathways and ontological categories. Via Biofilter 2.0 researchers can: • Annotate genomic location or region based data, such as results from association studies, or CNV analyses, with relevant biological knowledge for deeper interpretation • Filter genomic location or region based data on biological criteria, such as filtering a series SNPs to retain only SNPs present in specific genes within specific pathways of interest • Generate Predictive Models for gene-gene, SNP-SNP, or CNV-CNV interactions based on biological information, with priority for models to be tested based on biological relevance, thus narrowing the search space and reducing multiple hypothesis

  14. Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation

    PubMed Central

    Sharma, Virag; Elghafari, Anas; Hiller, Michael

    2016-01-01

    Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes. PMID:27016733

  15. Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation.

    PubMed

    Sharma, Virag; Elghafari, Anas; Hiller, Michael

    2016-06-20

    Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes. PMID:27016733

  16. An agent-based system for re-annotation of genomes.

    PubMed

    Nascimento, Leonardo Vianna do; Bazzan, Ana L C

    2005-01-01

    Genome annotation projects can produce incorrect results if they are based on obsolete data or inappropriate models. We have developed an automatic re-annotation system that uses agents to perform repetitive tasks and reports the results to the user. These tasks involve BLAST searches on biological databases (GenBank) and the use of detection tools (Genemark and Glimmer) to identify new open reading frames. Several agents execute these tools and combine their results to produce a list of open reading frames that is sent back to the user. Our goal was to reduce the manual work, executing most tasks automatically by computational tools. A prototype was implemented and validated using Mycoplasma pneumoniae and Haemophilus influenzae original annotated genomes. The results reported by the system identify most of new features present in the re-annotated versions of these genomes. PMID:16342042

  17. Annotating the Function of the Human Genome with Gene Ontology and Disease Ontology

    PubMed Central

    Hu, Yang; Zhou, Wenyang; Ren, Jun; Dong, Lixiang

    2016-01-01

    Increasing evidences indicated that function annotation of human genome in molecular level and phenotype level is very important for systematic analysis of genes. In this study, we presented a framework named Gene2Function to annotate Gene Reference into Functions (GeneRIFs), in which each functional description of GeneRIFs could be annotated by a text mining tool Open Biomedical Annotator (OBA), and each Entrez gene could be mapped to Human Genome Organisation Gene Nomenclature Committee (HGNC) gene symbol. After annotating all the records about human genes of GeneRIFs, 288,869 associations between 13,148 mRNAs and 7,182 terms, 9,496 associations between 948 microRNAs and 533 terms, and 901 associations between 139 long noncoding RNAs (lncRNAs) and 297 terms were obtained as a comprehensive annotation resource of human genome. High consistency of term frequency of individual gene (Pearson correlation = 0.6401, p = 2.2e − 16) and gene frequency of individual term (Pearson correlation = 0.1298, p = 3.686e − 14) in GeneRIFs and GOA shows our annotation resource is very reliable.

  18. A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data.

    PubMed

    Lu, Qiongshi; Hu, Yiming; Sun, Jiehuan; Cheng, Yuwei; Cheung, Kei-Hoi; Zhao, Hongyu

    2015-01-01

    Identifying functional regions in the human genome is a major goal in human genetics. Great efforts have been made to functionally annotate the human genome either through computational predictions, such as genomic conservation, or high-throughput experiments, such as the ENCODE project. These efforts have resulted in a rich collection of functional annotation data of diverse types that need to be jointly analyzed for integrated interpretation and annotation. Here we present GenoCanyon, a whole-genome annotation method that performs unsupervised statistical learning using 22 computational and experimental annotations thereby inferring the functional potential of each position in the human genome. With GenoCanyon, we are able to predict many of the known functional regions. The ability of predicting functional regions as well as its generalizable statistical framework makes GenoCanyon a unique and powerful tool for whole-genome annotation. The GenoCanyon web server is available at http://genocanyon.med.yale.edu. PMID:26015273

  19. Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies

    PubMed Central

    Platt, Roy N.; Blanco-Berdugo, Laura; Ray, David A.

    2016-01-01

    Transposable elements (TEs) are mobile genetic elements with the ability to replicate themselves throughout the host genome. In some taxa TEs reach copy numbers in hundreds of thousands and can occupy more than half of the genome. The increasing number of reference genomes from nonmodel species has begun to outpace efforts to identify and annotate TE content and methods that are used vary significantly between projects. Here, we demonstrate variation that arises in TE annotations when less than optimal methods are used. We found that across a variety of taxa, the ability to accurately identify TEs based solely on homology decreased as the phylogenetic distance between the queried genome and a reference increased. Next we annotated repeats using homology alone, as is often the case in new genome analyses, and a combination of homology and de novo methods as well as an additional manual curation step. Reannotation using these methods identified a substantial number of new TE subfamilies in previously characterized genomes, recognized a higher proportion of the genome as repetitive, and decreased the average genetic distance within TE families, implying recent TE accumulation. Finally, these finding—increased recognition of younger TEs—were confirmed via an analysis of the postman butterfly (Heliconius melpomene). These observations imply that complete TE annotation relies on a combination of homology and de novo–based repeat identification, manual curation, and classification and that relying on simple, homology-based methods is insufficient to accurately describe the TE landscape of a newly sequenced genome. PMID:26802115

  20. Finished Annotated Genome Sequence of Burkholderia pseudomallei Strain Bp1651, a Multidrug-Resistant Clinical Isolate

    PubMed Central

    Sue, David; Hakovirta, Janetta; Loparev, Vladimir N.; Knipe, Kristen; Sammons, Scott A.; Ranganathan-Ganakammal, Satishkumar; Changayil, Shankar; Srinivasamoorthy, Ganesh; Weil, Michael R.; Tatusov, Roman L.; Gee, Jay E.; Elrod, Mindy G.; Hoffmaster, Alex R.; Weigel, Linda M.

    2015-01-01

    Burkholderia pseudomallei strain Bp1651, a human isolate, is resistant to all clinically relevant antibiotics. We report here on the finished genome sequence assembly and annotation of the two chromosomes of this strain. This genome sequence may assist in understanding the mechanisms of antimicrobial resistance for this pathogenic species. PMID:26634765

  1. Using Microbial Genome Annotation as a Foundation for Collaborative Student Research

    ERIC Educational Resources Information Center

    Reed, Kelynne E.; Richardson, John M.

    2013-01-01

    We used the Integrated Microbial Genomes Annotation Collaboration Toolkit as a framework to incorporate microbial genomics research into a microbiology and biochemistry course in a way that promoted student learning of bioinformatics and research skills and emphasized teamwork and collaboration as evidenced through multiple assessment mechanisms.…

  2. The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

    PubMed Central

    2009-01-01

    The Gene Ontology (GO) is a collaborative effort that provides structured vocabularies for annotating the molecular function, biological role, and cellular location of gene products in a highly systematic way and in a species-neutral manner with the aim of unifying the representation of gene function across different organisms. Each contributing member of the GO Consortium independently associates GO terms to gene products from the organism(s) they are annotating. Here we introduce the Reference Genome project, which brings together those independent efforts into a unified framework based on the evolutionary relationships between genes in these different organisms. The Reference Genome project has two primary goals: to increase the depth and breadth of annotations for genes in each of the organisms in the project, and to create data sets and tools that enable other genome annotation efforts to infer GO annotations for homologous genes in their organisms. In addition, the project has several important incidental benefits, such as increasing annotation consistency across genome databases, and providing important improvements to the GO's logical structure and biological content. PMID:19578431

  3. Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome

    NASA Astrophysics Data System (ADS)

    Ernst, Jason; Kellis, Manolis

    A plethora of epigenetic modifications have been described in the human genome and shown to play diverse roles in gene regulation, cellular differentiation and the onset of disease. Although individual modifications have been linked to the activity levels of various genetic functional elements, their combinatorial patterns are still unresolved and their potential for systematic de novo genome annotation remains untapped. Here, we use a multivariate Hidden Markov Model to reveal chromatin states in human T cells, based on recurrent and spatially coherent combinations of chromatin marks.We define 51 distinct chromatin states, including promoter-associated, transcription-associated, active intergenic, largescale repressed and repeat-associated states. Each chromatin state shows specific enrichments in functional annotations, sequence motifs and specific experimentally observed characteristics, suggesting distinct biological roles. This approach provides a complementary functional annotation of the human genome that reveals the genome-wide locations of diverse classes of epigenetic function.

  4. AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome

    PubMed Central

    Legeai, Fabrice; Shigenobu, Shuji; Gauthier, Jean-Pierre; Colbourne, John; Rispe, Claude; Collin, Olivier; Richards, Stephen; Wilson, Alex C. C.; Tagu, Denis

    2015-01-01

    AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com. PMID:20482635

  5. Improvement of whole-genome annotation of cereals through comparative analyses

    PubMed Central

    Zhu, Wei; Buell, C. Robin

    2007-01-01

    Rice is an important model species for the Poaceae and other monocotyledonous plants. With the availability of a near-complete, finished, and annotated rice genome, we performed genome level comparisons between rice and all plant species in which large genomic or transcriptomic data sets are available to determine the utility of cross-species sequence for structural and functional annotation of the rice genome. Through comparative analyses with four plant genome sequence data sets and transcript assemblies from 185 plant species, we were able to confirm and improve the structural annotation of the rice genome. Support for 38,109 (89.3%) of the total 42,653 nontransposable element-related genes in the rice genome in the form of a rice expressed sequence tag, full-length cDNA, or plant homolog from our comparative analyses could be found. Although the majority of the putative homologs were obtained from Poaceae species, putative homologs were identified in dicotyledonous angiosperms, gymnosperms, and other plants such as algae, moss, and fern. A set of rice genes (7669) lacking a putative homolog was identified which may be lineage-specific genes that evolved after speciation and have a role in species diversity. Improvements to the current rice gene structural annotation could be identified from our comparative alignments and we were able to identify 487 genes which were mostly likely missed in the current rice genome annotation and another 500 genes for structural annotation review. We were able to demonstrate the utility of cross-species comparative alignments in the identification of noncoding sequences and in confirmation of gene nesting in rice. PMID:17284677

  6. A SPECTRAL APPROACH INTEGRATING FUNCTIONAL GENOMIC ANNOTATIONS FOR CODING AND NONCODING VARIANTS

    PubMed Central

    IONITA-LAZA, IULIANA; MCCALLUM, KENNETH; XU, BIN; BUXBAUM, JOSEPH

    2015-01-01

    Over the past few years, substantial effort has been put into the functional annotation of variation in human genome sequence. Such annotations can play a critical role in identifying putatively causal variants among the abundant natural variation that occurs at a locus of interest. The main challenges in using these various annotations include their large numbers, and their diversity. Here we develop an unsupervised approach to integrate these different annotations into one measure of functional importance (Eigen), that, unlike most existing methods, is not based on any labeled training data. We show that the resulting meta-score has better discriminatory ability using disease associated and putatively benign variants from published studies (in both coding and noncoding regions) compared with the recently proposed CADD score. Across varied scenarios, the Eigen score performs generally better than any single individual annotation, representing a powerful single functional score that can be incorporated in fine-mapping studies. PMID:26727659

  7. Creating reference gene annotation for the mouse C57BL6/J genome assembly.

    PubMed

    Mudge, Jonathan M; Harrow, Jennifer

    2015-10-01

    Annotation on the reference genome of the C57BL6/J mouse has been an ongoing project ever since the draft genome was first published. Initially, the principle focus was on the identification of all protein-coding genes, although today the importance of describing long non-coding RNAs, small RNAs, and pseudogenes is recognized. Here, we describe the progress of the GENCODE mouse annotation project, which combines manual annotation from the HAVANA group with Ensembl computational annotation, alongside experimental and in silico validation pipelines from other members of the consortium. We discuss the more recent incorporation of next-generation sequencing datasets into this workflow, including the usage of mass-spectrometry data to potentially identify novel protein-coding genes. Finally, we will outline how the C57BL6/J genebuild can be used to gain insights into the variant sites that distinguish different mouse strains and species. PMID:26187010

  8. Companion: a web server for annotation and analysis of parasite genomes.

    PubMed

    Steinbiss, Sascha; Silva-Franco, Fatima; Brunk, Brian; Foth, Bernardo; Hertz-Fowler, Christiane; Berriman, Matthew; Otto, Thomas D

    2016-07-01

    Currently available sequencing technologies enable quick and economical sequencing of many new eukaryotic parasite (apicomplexan or kinetoplastid) species or strains. Compared to SNP calling approaches, de novo assembly of these genomes enables researchers to additionally determine insertion, deletion and recombination events as well as to detect complex sequence diversity, such as that seen in variable multigene families. However, there currently are no automated eukaryotic annotation pipelines offering the required range of results to facilitate such analyses. A suitable pipeline needs to perform evidence-supported gene finding as well as functional annotation and pseudogene detection up to the generation of output ready to be submitted to a public database. Moreover, no current tool includes quick yet informative comparative analyses and a first pass visualization of both annotation and analysis results. To overcome those needs we have developed the Companion web server (http://companion.sanger.ac.uk) providing parasite genome annotation as a service using a reference-based approach. We demonstrate the use and performance of Companion by annotating two Leishmania and Plasmodium genomes as typical parasite cases and evaluate the results compared to manually annotated references. PMID:27105845

  9. Annotation methods to develop and evaluate an expert system based on natural language processing in electronic medical records.

    PubMed

    Gicquel, Quentin; Tvardik, Nastassia; Bouvry, Côme; Kergourlay, Ivan; Bittar, André; Segond, Frédérique; Darmoni, Stefan; Metzger, Marie-Hélène

    2015-01-01

    The objective of the SYNODOS collaborative project was to develop a generic IT solution, combining a medical terminology server, a semantic analyser and a knowledge base. The goal of the project was to generate meaningful epidemiological data for various medical domains from the textual content of French medical records. In the context of this project, we built a care pathway oriented conceptual model and corresponding annotation method to develop and evaluate an expert system's knowledge base. The annotation method is based on a semi-automatic process, using a software application (MedIndex). This application exchanges with a cross-lingual multi-termino-ontology portal. The annotator selects the most appropriate medical code proposed for the medical concept in question by the multi-termino-ontology portal and temporally labels the medical concept according to the course of the medical event. This choice of conceptual model and annotation method aims to create a generic database of facts for the secondary use of electronic health records data. PMID:26262366

  10. Genome-wide functional annotation of Phomopsis longicolla isolate MSPL 10-6.

    PubMed

    Darwish, Omar; Li, Shuxian; Matthews, Benjamin; Alkharouf, Nadim

    2016-06-01

    Phomopsis seed decay of soybean is caused primarily by the seed-borne fungal pathogen Phomopsis longicolla (syn. Diaporthe longicolla). This disease severely decreases soybean seed quality, reduces seedling vigor and stand establishment, and suppresses yield. It is one of the most economically important soybean diseases. In this study we annotated the entire genome of P. longicolla isolate MSPL 10-6, which was isolated from field-grown soybean seed in Mississippi, USA. This study represents the first reported genome-wide functional annotation of a seed borne fungal pathogen in the Diaporthe-Phomopsis complex. The P. longicolla genome annotation will enable research into the genetic basis of fungal infection of soybean seed and provide information for the study of soybean-fungal interactions. The genome annotation will also be a valuable resource for the research and agricultural communities. It will aid in the development of new control strategies for this pathogen. The annotations can be found from: http://bioinformatics.towson.edu/phomopsis_longicolla/download.html. NCBI accession number is: AYRD00000000. PMID:27222801

  11. Whole genome sequence and genome annotation of Colletotrichum acutatum, causal agent of anthracnose in pepper plants in South Korea

    PubMed Central

    Han, Joon-Hee; Chon, Jae-Kyung; Ahn, Jong-Hwa; Choi, Ik-Young; Lee, Yong-Hwan; Kim, Kyoung Su

    2016-01-01

    Colletotrichum acutatum is a destructive fungal pathogen which causes anthracnose in a wide range of crops. Here we report the whole genome sequence and annotation of C. acutatum strain KC05, isolated from an infected pepper in Kangwon, South Korea. Genomic DNA from the KC05 strain was used for the whole genome sequencing using a PacBio sequencer and the MiSeq system. The KC05 genome was determined to be 52,190,760 bp in size with a G + C content of 51.73% in 27 scaffolds and to contain 13,559 genes with an average length of 1516 bp. Gene prediction and annotation were performed by incorporating RNA-Seq data. The genome sequence of the KC05 was deposited at DDBJ/ENA/GenBank under the accession number LUXP00000000. PMID:27114908

  12. Whole genome sequence and genome annotation of Colletotrichum acutatum, causal agent of anthracnose in pepper plants in South Korea.

    PubMed

    Han, Joon-Hee; Chon, Jae-Kyung; Ahn, Jong-Hwa; Choi, Ik-Young; Lee, Yong-Hwan; Kim, Kyoung Su

    2016-06-01

    Colletotrichum acutatum is a destructive fungal pathogen which causes anthracnose in a wide range of crops. Here we report the whole genome sequence and annotation of C. acutatum strain KC05, isolated from an infected pepper in Kangwon, South Korea. Genomic DNA from the KC05 strain was used for the whole genome sequencing using a PacBio sequencer and the MiSeq system. The KC05 genome was determined to be 52,190,760 bp in size with a G + C content of 51.73% in 27 scaffolds and to contain 13,559 genes with an average length of 1516 bp. Gene prediction and annotation were performed by incorporating RNA-Seq data. The genome sequence of the KC05 was deposited at DDBJ/ENA/GenBank under the accession number LUXP00000000. PMID:27114908

  13. Data for constructing insect genome content matrices for phylogenetic analysis and functional annotation.

    PubMed

    Rosenfeld, Jeffrey; Foox, Jonathan; DeSalle, Rob

    2016-03-01

    Twenty one fully sequenced and well annotated insect genomes were used to construct genome content matrices for phylogenetic analysis and functional annotation of insect genomes. To examine the role of e-value cutoff in ortholog determination we used scaled e-value cutoffs and a single linkage clustering approach.. The present communication includes (1) a list of the genomes used to construct the genome content phylogenetic matrices, (2) a nexus file with the data matrices used in phylogenetic analysis, (3) a nexus file with the Newick trees generated by phylogenetic analysis, (4) an excel file listing the Core (CORE) genes and Unique (UNI) genes found in five insect groups, and (5) a figure showing a plot of consistency index (CI) versus percent of unannotated genes that are apomorphies in the data set for gene losses and gains and bar plots of gains and losses for four consistency index (CI) cutoffs. PMID:26862572

  14. Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis.

    PubMed

    Kelkar, Dhanashree S; Provost, Elayne; Chaerkady, Raghothama; Muthusamy, Babylakshmi; Manda, Srikanth S; Subbannayya, Tejaswini; Selvan, Lakshmi Dhevi N; Wang, Chieh-Huei; Datta, Keshava K; Woo, Sunghee; Dwivedi, Sutopa B; Renuse, Santosh; Getnet, Derese; Huang, Tai-Chung; Kim, Min-Sik; Pinto, Sneha M; Mitchell, Christopher J; Madugundu, Anil K; Kumar, Praveen; Sharma, Jyoti; Advani, Jayshree; Dey, Gourav; Balakrishnan, Lavanya; Syed, Nazia; Nanjappa, Vishalakshi; Subbannayya, Yashwanth; Goel, Renu; Prasad, T S Keshava; Bafna, Vineet; Sirdeshmukh, Ravi; Gowda, Harsha; Wang, Charles; Leach, Steven D; Pandey, Akhilesh

    2014-11-01

    Accurate annotation of protein-coding genes is one of the primary tasks upon the completion of whole genome sequencing of any organism. In this study, we used an integrated transcriptomic and proteomic strategy to validate and improve the existing zebrafish genome annotation. We undertook high-resolution mass-spectrometry-based proteomic profiling of 10 adult organs, whole adult fish body, and two developmental stages of zebrafish (SAT line), in addition to transcriptomic profiling of six organs. More than 7,000 proteins were identified from proteomic analyses, and ∼ 69,000 high-confidence transcripts were assembled from the RNA sequencing data. Approximately 15% of the transcripts mapped to intergenic regions, the majority of which are likely long non-coding RNAs. These high-quality transcriptomic and proteomic data were used to manually reannotate the zebrafish genome. We report the identification of 157 novel protein-coding genes. In addition, our data led to modification of existing gene structures including novel exons, changes in exon coordinates, changes in frame of translation, translation in annotated UTRs, and joining of genes. Finally, we discovered four instances of genome assembly errors that were supported by both proteomic and transcriptomic data. Our study shows how an integrative analysis of the transcriptome and the proteome can extend our understanding of even well-annotated genomes. PMID:25060758

  15. Segtor: Rapid Annotation of Genomic Coordinates and Single Nucleotide Variations Using Segment Trees

    PubMed Central

    Renaud, Gabriel; Neves, Pedro; Folador, Edson Luiz; Ferreira, Carlos Gil; Passetti, Fabio

    2011-01-01

    Various research projects often involve determining the relative position of genomic coordinates, intervals, single nucleotide variations (SNVs), insertions, deletions and translocations with respect to genes and their potential impact on protein translation. Due to the tremendous increase in throughput brought by the use of next-generation sequencing, investigators are routinely faced with the need to annotate very large datasets. We present Segtor, a tool to annotate large sets of genomic coordinates, intervals, SNVs, indels and translocations. Our tool uses segment trees built using the start and end coordinates of the genomic features the user wishes to use instead of storing them in a database management system. The software also produces annotation statistics to allow users to visualize how many coordinates were found within various portions of genes. Our system currently can be made to work with any species available on the UCSC Genome Browser. Segtor is a suitable tool for groups, especially those with limited access to programmers or with interest to analyze large amounts of individual genomes, who wish to determine the relative position of very large sets of mapped reads and subsequently annotate observed mutations between the reads and the reference. Segtor (http://lbbc.inca.gov.br/segtor/) is an open-source tool that can be freely downloaded for non-profit use. We also provide a web interface for testing purposes. PMID:22069465

  16. High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic mode...

  17. Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes.

    PubMed

    Ockendon, Nina F; O'Connell, Lauren A; Bush, Stephen J; Monzón-Sandoval, Jimena; Barnes, Holly; Székely, Tamás; Hofmann, Hans A; Dorus, Steve; Urrutia, Araxi O

    2016-03-01

    Next-generation sequencing methods, such as RNA-seq, have permitted the exploration of gene expression in a range of organisms which have been studied in ecological contexts but lack a sequenced genome. However, the efficacy and accuracy of RNA-seq annotation methods using reference genomes from related species have yet to be robustly characterized. Here we conduct a comprehensive power analysis employing RNA-seq data from Drosophila melanogaster in conjunction with 11 additional genomes from related Drosophila species to compare annotation methods and quantify the impact of evolutionary divergence between transcriptome and the reference genome. Our analyses demonstrate that, regardless of the level of sequence divergence, direct genome mapping (DGM), where transcript short reads are aligned directly to the reference genome, significantly outperforms the widely used de novo and guided assembly-based methods in both the quantity and accuracy of gene detection. Our analysis also reveals that DGM recovers a more representative profile of Gene Ontology functional categories, which are often used to interpret emergent patterns in genomewide expression analyses. Lastly, analysis of available primate RNA-seq data demonstrates the applicability of our observations across diverse taxa. Our quantification of annotation accuracy and reduced gene detection associated with sequence divergence thus provides empirically derived guidelines for the design of future gene expression studies in species without sequenced genomes. PMID:26358618

  18. Genome sequencing and annotation of Proteus sp. SAS71

    PubMed Central

    Selim, Samy; Hassan, Sherif; Hagagy, Nashwa

    2015-01-01

    We report draft genome sequence of Proteus sp. strain SAS71, isolated from water spring in Aljouf region, Saudi Arabia. The draft genome size is 3,037,704 bp with a G + C content of 39.3% and contains 6 rRNA sequence (single copies of 5S, 16S & 23S rRNA). The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LDIU00000000. PMID:26697338

  19. Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes.

    PubMed

    Shim, Donghwan; Park, Sin-Gi; Kim, Kangmin; Bae, Wonsil; Lee, Gir Won; Ha, Byeong-Suk; Ro, Hyeon-Su; Kim, Myungkil; Ryoo, Rhim; Rhee, Sung-Keun; Nou, Ill-Sup; Koo, Chang-Duck; Hong, Chang Pyo; Ryu, Hojin

    2016-04-10

    Lentinula edodes, the popular shiitake mushroom, is one of the most important cultivated edible mushrooms. It is used as a food and for medicinal purposes. Here, we present the 46.1Mb draft genome of L. edodes, comprising 13,028 predicted gene models. The genome assembly consists of 31 scaffolds. Gene annotation provides key information about various signaling pathways and secondary metabolites. This genomic information should help establish the molecular genetic markers for MAS/MAB and increase our understanding of the genome structure and function. PMID:26924240

  20. The draft genome sequence and annotation of the desert woodrat Neotoma lepida.

    PubMed

    Campbell, Michael; Oakeson, Kelly F; Yandell, Mark; Halpert, James R; Dearing, Denise

    2016-09-01

    We present the de novo draft genome sequence for a vertebrate mammalian herbivore, the desert woodrat (Neotoma lepida). This species is of ecological and evolutionary interest with respect to ingestion, microbial detoxification and hepatic metabolism of toxic plant secondary compounds from the highly toxic creosote bush (Larrea tridentata) and the juniper shrub (Juniperus monosperma). The draft genome sequence and annotation have been deposited at GenBank under the accession LZPO01000000. PMID:27408812

  1. Toward an Upgraded Honey Bee (Apis mellifera L.) Genome Annotation Using Proteogenomics.

    PubMed

    McAfee, Alison; Harpur, Brock A; Michaud, Sarah; Beavis, Ronald C; Kent, Clement F; Zayed, Amro; Foster, Leonard J

    2016-02-01

    The honey bee is a key pollinator in agricultural operations as well as a model organism for studying the genetics and evolution of social behavior. The Apis mellifera genome has been sequenced and annotated twice over, enabling proteomics and functional genomics methods for probing relevant aspects of their biology. One troubling trend that emerged from proteomic analyses is that honey bee peptide samples consistently result in lower peptide identification rates compared with other organisms. This suggests that the genome annotation can be improved, or atypical biological processes are interfering with the mass spectrometry workflow. First, we tested whether high levels of polymorphisms could explain some of the missed identifications by searching spectra against the reference proteome (OGSv3.2) versus a customized proteome of a single honey bee, but our results indicate that this contribution was minor. Likewise, error-tolerant peptide searches lead us to eliminate unexpected post-translational modifications as a major factor in missed identifications. We then used a proteogenomic approach with ∼1500 raw files to search for missing genes and new exons, to revive discarded annotations and to identify over 2000 new coding regions. These results will contribute to a more comprehensive genome annotation and facilitate continued research on this important insect. PMID:26718741

  2. Draft Genome Sequence and Gene Annotation of the Uropathogenic Bacterium Proteus mirabilis Pr2921

    PubMed Central

    Giorello, F. M.; Romero, V.; Farias, J.; Scavone, P.; Umpiérrez, A.; Zunino, P.

    2016-01-01

    Here, we report the genome sequence of Proteus mirabilis Pr2921, a uropathogenic bacterium that can cause severe complicated urinary tract infections. After gene annotation, we identified two additional copies of ucaA, one of the most studied fimbrial protein genes, and other fimbriae related-proteins that are not present in P. mirabilis HI4320. PMID:27340058

  3. Complete Genome Sequence and Annotation of the Treponema pallidum subsp. pallidum Chicago Strain ▿

    PubMed Central

    Giacani, Lorenzo; Jeffrey, Brendan M.; Molini, Barbara J.; Le, HoaVan T.; Lukehart, Sheila A.; Centurion-Lara, Arturo; Rockey, Daniel D.

    2010-01-01

    In syphilis research, the Nichols strain of Treponema pallidum, isolated in 1912, has been the most widely studied. Recently, important differences among T. pallidum strains emerged; therefore, we sequenced and annotated the Chicago strain genome to facilitate and encourage the use of this strain in studying the pathogenesis of syphilis. PMID:20348263

  4. Draft Genome Sequence and Gene Annotation of Stemphylium lycopersici Strain CIDEFI-216

    PubMed Central

    Franco, Mario E. E.; López, Silvina; Medina, Rocio; Saparrat, Mario C. N.

    2015-01-01

    Stemphylium lycopersici is a plant-pathogenic fungus that is widely distributed throughout the world. In tomatoes, it is one of the etiological agents of gray leaf spot disease. Here, we report the first draft genome sequence of S. lycopersici, including its gene structure and functional annotation. PMID:26404600

  5. Genome Sequence and Annotation of Colletotrichum higginsianum, a Causal Agent of Crucifer Anthracnose Disease.

    PubMed

    Zampounis, Antonios; Pigné, Sandrine; Dallery, Jean-Félix; Wittenberg, Alexander H J; Zhou, Shiguo; Schwartz, David C; Thon, Michael R; O'Connell, Richard J

    2016-01-01

    Colletotrichum higginsianum is an ascomycete fungus causing anthracnose disease on numerous cultivated plants in the family Brassicaceae, as well as the model plant Arabidopsis thaliana We report an assembly of the nuclear genome and gene annotation of this pathogen, which was obtained using a combination of PacBio long-read sequencing and optical mapping. PMID:27540062

  6. Genome Sequence and Annotation of Colletotrichum higginsianum, a Causal Agent of Crucifer Anthracnose Disease

    PubMed Central

    Zampounis, Antonios; Pigné, Sandrine; Dallery, Jean-Félix; Wittenberg, Alexander H. J.; Zhou, Shiguo; Schwartz, David C.

    2016-01-01

    Colletotrichum higginsianum is an ascomycete fungus causing anthracnose disease on numerous cultivated plants in the family Brassicaceae, as well as the model plant Arabidopsis thaliana. We report an assembly of the nuclear genome and gene annotation of this pathogen, which was obtained using a combination of PacBio long-read sequencing and optical mapping. PMID:27540062

  7. ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins

    PubMed Central

    Mall, Tarun; Eckstein, John; Norris, David; Vora, Hiral; Freese, Nowlan H.; Loraine, Ann E.

    2016-01-01

    Summary: One gene can produce multiple transcript variants encoding proteins with different functions. To facilitate visual analysis of transcript variants, we developed ProtAnnot, which shows protein annotations in the context of genomic sequence. ProtAnnot searches InterPro and displays profile matches (protein annotations) alongside gene models, exposing how alternative promoters, splicing and 3′ end processing add, remove, or remodel functional motifs. To draw attention to these effects, ProtAnnot color-codes exons by frame and displays a cityscape graphic summarizing exonic sequence at each position. These techniques make visual analysis of alternative transcripts faster and more convenient for biologists. Availability and implementation: ProtAnnot is a plug-in App for Integrated Genome Browser, an open source desktop genome browser available from http://www.bioviz.org. Contact: aloraine@uncc.edu PMID:27153567

  8. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

    PubMed

    Sakai, Hiroaki; Lee, Sung Shin; Tanaka, Tsuyoshi; Numa, Hisataka; Kim, Jungsok; Kawahara, Yoshihiro; Wakimoto, Hironobu; Yang, Ching-chia; Iwamoto, Masao; Abe, Takashi; Yamada, Yuko; Muto, Akira; Inokuchi, Hachiro; Ikemura, Toshimichi; Matsumoto, Takashi; Sasaki, Takuji; Itoh, Takeshi

    2013-02-01

    The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics. PMID:23299411

  9. Resources for Biological Annotation of the Drosophila Genome

    SciTech Connect

    Gerald M. Rubin

    2005-08-08

    This project supported seed money for the development of cDNA and genetic resources to support studies of the Drosophila melanogaster genome. Key publications supported by this work that provide additional detail: (1) ''The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes''; and (2) ''The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes''.

  10. Using genomic annotations increases statistical power to detect eGenes

    PubMed Central

    Duong, Dat; Zou, Jennifer; Hormozdiari, Farhad; Sul, Jae Hoon; Ernst, Jason; Han, Buhm; Eskin, Eleazar

    2016-01-01

    Motivation: Expression quantitative trait loci (eQTLs) are genetic variants that affect gene expression. In eQTL studies, one important task is to find eGenes or genes whose expressions are associated with at least one eQTL. The standard statistical method to determine whether a gene is an eGene requires association testing at all nearby variants and the permutation test to correct for multiple testing. The standard method however does not consider genomic annotation of the variants. In practice, variants near gene transcription start sites (TSSs) or certain histone modifications are likely to regulate gene expression. In this article, we introduce a novel eGene detection method that considers this empirical evidence and thereby increases the statistical power. Results: We applied our method to the liver Genotype-Tissue Expression (GTEx) data using distance from TSSs, DNase hypersensitivity sites, and six histone modifications as the genomic annotations for the variants. Each of these annotations helped us detected more candidate eGenes. Distance from TSS appears to be the most important annotation; specifically, using this annotation, our method discovered 50% more candidate eGenes than the standard permutation method. Contact: buhm.han@amc.seoul.kr or eeskin@cs.ucla.edu PMID:27307612

  11. Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data.

    PubMed

    Lohse, Marc; Nagel, Axel; Herter, Thomas; May, Patrick; Schroda, Michael; Zrenner, Rita; Tohge, Takayuki; Fernie, Alisdair R; Stitt, Mark; Usadel, Björn

    2014-05-01

    Next-generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan 'BIN' ontology, which is tailored for functional annotation of plant 'omics' data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan-to-GO translation table to export results as GO terms. Mercator is available free of charge via http://mapman.gabipd.org/web/guest/app/Mercator. PMID:24237261

  12. An Integrative Method for Identifying the Over-Annotated Protein-Coding Genes in Microbial Genomes

    PubMed Central

    Yu, Jia-Feng; Xiao, Ke; Jiang, Dong-Ke; Guo, Jing; Wang, Ji-Hua; Sun, Xiao

    2011-01-01

    The falsely annotated protein-coding genes have been deemed one of the major causes accounting for the annotating errors in public databases. Although many filtering approaches have been designed for the over-annotated protein-coding genes, some are questionable due to the resultant increase in false negative. Furthermore, there is no webserver or software specifically devised for the problem of over-annotation. In this study, we propose an integrative algorithm for detecting the over-annotated protein-coding genes in microorganisms. Overall, an average accuracy of 99.94% is achieved over 61 microbial genomes. The extremely high accuracy indicates that the presented algorithm is efficient to differentiate the protein-coding genes from the non-coding open reading frames. Abundant analyses show that the predicting results are reliable and the integrative algorithm is robust and convenient. Our analysis also indicates that the over-annotated protein-coding genes can cause the false positive of horizontal gene transfers detection. The webserver of the proposed algorithm can be freely accessible from www.cbi.seu.edu.cn/RPGM. PMID:21903723

  13. High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.

    PubMed

    Seaver, Samuel M D; Gerdes, Svetlana; Frelin, Océane; Lerma-Ortiz, Claudia; Bradbury, Louis M T; Zallot, Rémi; Hasnain, Ghulam; Niehaus, Thomas D; El Yacoubi, Basma; Pasternak, Shiran; Olson, Robert; Pusch, Gordon; Overbeek, Ross; Stevens, Rick; de Crécy-Lagard, Valérie; Ware, Doreen; Hanson, Andrew D; Henry, Christopher S

    2014-07-01

    The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed. PMID:24927599

  14. Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci

    PubMed Central

    Trynka, Gosia; Westra, Harm-Jan; Slowikowski, Kamil; Hu, Xinli; Xu, Han; Stranger, Barbara E.; Klein, Robert J.; Han, Buhm; Raychaudhuri, Soumya

    2015-01-01

    Identifying genomic annotations that differentiate causal from trait-associated variants is essential to fine mapping disease loci. Although many studies have identified non-coding functional annotations that overlap disease-associated variants, these annotations often colocalize, complicating the ability to use these annotations for fine mapping causal variation. We developed a statistical approach (Genomic Annotation Shifter [GoShifter]) to assess whether enriched annotations are able to prioritize causal variation. GoShifter defines the null distribution of an annotation overlapping an allele by locally shifting annotations; this approach is less sensitive to biases arising from local genomic structure than commonly used enrichment methods that depend on SNP matching. Local shifting also allows GoShifter to identify independent causal effects from colocalizing annotations. Using GoShifter, we confirmed that variants in expression quantitative trail loci drive gene-expression changes though DNase-I hypersensitive sites (DHSs) near transcription start sites and independently through 3′ UTR regulation. We also showed that (1) 15%–36% of trait-associated loci map to DHSs independently of other annotations; (2) loci associated with breast cancer and rheumatoid arthritis harbor potentially causal variants near the summits of histone marks rather than full peak bodies; (3) variants associated with height are highly enriched in embryonic stem cell DHSs; and (4) we can effectively prioritize causal variation at specific loci. PMID:26140449

  15. Genome sequencing and annotation of Amycolatopsis azurea DSM 43854(T).

    PubMed

    Khatri, Indu; Subramanian, Srikrishna; Mayilraj, Shanmugam

    2014-12-01

    We report the 9.2 Mb genome of the azureomycin A and B antibiotic producing strain Amycolatopsis azurea isolated from a Japanese soil sample. The draft genome of strain DSM 43854(T) consists of 9,223,451 bp with a G + C content of 69.0% and the genome contains 3 rRNA genes (5S-23S-16S) and 58 aminoacyl-tRNA synthetase genes. The homology searches revealed that the PKS gene clusters are supposed to be responsible for the biosynthesis of naptomycin, macbecin, rifamycin, mitomycin, maduropeptin enediyne, neocarzinostatin enediyne, C-1027 enediyne, calicheamicin enediyne, landomycin, simocyclinone, medermycin, granaticin, polyketomycin, teicoplanin, balhimycin, vancomycin, staurosporine, rubradirin and complestatin. PMID:26484067

  16. Genome sequencing and annotation of Amycolatopsis azurea DSM 43854T

    PubMed Central

    Khatri, Indu; Subramanian, Srikrishna; Mayilraj, Shanmugam

    2014-01-01

    We report the 9.2 Mb genome of the azureomycin A and B antibiotic producing strain Amycolatopsis azurea isolated from a Japanese soil sample. The draft genome of strain DSM 43854T consists of 9,223,451 bp with a G + C content of 69.0% and the genome contains 3 rRNA genes (5S–23S–16S) and 58 aminoacyl-tRNA synthetase genes. The homology searches revealed that the PKS gene clusters are supposed to be responsible for the biosynthesis of naptomycin, macbecin, rifamycin, mitomycin, maduropeptin enediyne, neocarzinostatin enediyne, C-1027 enediyne, calicheamicin enediyne, landomycin, simocyclinone, medermycin, granaticin, polyketomycin, teicoplanin, balhimycin, vancomycin, staurosporine, rubradirin and complestatin. PMID:26484067

  17. An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3

    PubMed Central

    2014-01-01

    When the genome of Ruegeria pomeroyi DSS-3 was published in 2004, it represented the first sequence from a heterotrophic marine bacterium. Over the last ten years, the strain has become a valuable model for understanding the cycling of sulfur and carbon in the ocean. To ensure that this genome remains useful, we have updated 69 genes to incorporate functional annotations based on new experimental data, and improved the identification of 120 protein-coding regions based on proteomic and transcriptomic data. We review the progress made in understanding the biology of R. pomeroyi DSS-3 and list the changes made to the genome. PMID:25780504

  18. Genome sequencing and annotation of multidrug resistant Mycobacterium tuberculosis (MDR-TB) PR10 strain

    PubMed Central

    Halim, Mohd Zakihalani A.; Jaafar, Mohammad Maaruf; Teh, Lay Kek; Ismail, Mohamad Izwan; Lee, Lian Shien; Ngeow, Yun Fong; Nor, Norazmi Mohd; Zainuddin, Zainul Fadziruddin; Tang, Thean Hock; Najimudin, Mohd Nazalan Mohd; Salleh, Mohd Zaki

    2016-01-01

    Here, we report the draft genome sequence and annotation of a multidrug resistant Mycobacterium tuberculosis strain PR10 (MDR-TB PR10) isolated from a patient diagnosed with tuberculosis. The size of the draft genome MDR-TB PR10 is 4.34 Mbp with 65.6% of G + C content and consists of 4637 predicted genes. The determinants were categorized by RAST into 400 subsystems with 4286 coding sequences and 50 RNAs. The whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number CP010968. PMID:26981419

  19. Genome sequencing and annotation of multidrug resistant Mycobacterium tuberculosis (MDR-TB) PR10 strain.

    PubMed

    Halim, Mohd Zakihalani A; Jaafar, Mohammad Maaruf; Teh, Lay Kek; Ismail, Mohamad Izwan; Lee, Lian Shien; Ngeow, Yun Fong; Nor, Norazmi Mohd; Zainuddin, Zainul Fadziruddin; Tang, Thean Hock; Najimudin, Mohd Nazalan Mohd; Salleh, Mohd Zaki

    2016-03-01

    Here, we report the draft genome sequence and annotation of a multidrug resistant Mycobacterium tuberculosis strain PR10 (MDR-TB PR10) isolated from a patient diagnosed with tuberculosis. The size of the draft genome MDR-TB PR10 is 4.34 Mbp with 65.6% of G + C content and consists of 4637 predicted genes. The determinants were categorized by RAST into 400 subsystems with 4286 coding sequences and 50 RNAs. The whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number CP010968. PMID:26981419

  20. Curation of the genome annotation of Pichia pastoris (Komagataella phaffii) CBS7435 from gene level to protein function.

    PubMed

    Valli, Minoska; Tatto, Nadine E; Peymann, Armin; Gruber, Clemens; Landes, Nils; Ekker, Heinz; Thallinger, Gerhard G; Mattanovich, Diethard; Gasser, Brigitte; Graf, Alexandra B

    2016-09-01

    As manually curated and non-automated BLAST analysis of the published Pichia pastoris genome sequences revealed many differences between the gene annotations of the strains GS115 and CBS7435, RNA-Seq analysis, supported by proteomics, was performed to improve the genome annotation. Detailed analysis of sequence alignment and protein domain predictions were made to extend the functional genome annotation to all P. pastoris sequences. This allowed the identification of 492 new ORFs, 4916 hypothetical UTRs and the correction of 341 incorrect ORF predictions, which were mainly due to the presence of upstream ATG or erroneous intron predictions. Moreover, 175 previously erroneously annotated ORFs need to be removed from the annotation. In total, we have annotated 5325 ORFs. Regarding the functionality of those genes, we improved all gene and protein descriptions. Thereby, the percentage of ORFs with functional annotation was increased from 48% to 73%. Furthermore, we defined functional groups, covering 25 biological cellular processes of interest, by grouping all genes that are part of the defined process. All data are presented in the newly launched genome browser and database available at www.pichiagenome.org In summary, we present a wide spectrum of curation of the P. pastoris genome annotation from gene level to protein function. PMID:27388471

  1. Woods: A fast and accurate functional annotator and classifier of genomic and metagenomic sequences.

    PubMed

    Sharma, Ashok K; Gupta, Ankit; Kumar, Sanjiv; Dhakan, Darshan B; Sharma, Vineet K

    2015-07-01

    Functional annotation of the gigantic metagenomic data is one of the major time-consuming and computationally demanding tasks, which is currently a bottleneck for the efficient analysis. The commonly used homology-based methods to functionally annotate and classify proteins are extremely slow. Therefore, to achieve faster and accurate functional annotation, we have developed an orthology-based functional classifier 'Woods' by using a combination of machine learning and similarity-based approaches. Woods displayed a precision of 98.79% on independent genomic dataset, 96.66% on simulated metagenomic dataset and >97% on two real metagenomic datasets. In addition, it performed >87 times faster than BLAST on the two real metagenomic datasets. Woods can be used as a highly efficient and accurate classifier with high-throughput capability which facilitates its usability on large metagenomic datasets. PMID:25863333

  2. Whole genome profiling physical map and ancestral annotation of tobacco Hicks Broadleaf

    PubMed Central

    Sierro, Nicolas; van Oeveren, Jan; van Eijk, Michiel J T; Martin, Florian; Stormo, Keith E; Peitsch, Manuel C; Ivanov, Nikolai V

    2013-01-01

    Genomics-based breeding of economically important crops such as banana, coffee, cotton, potato, tobacco and wheat is often hampered by genome size, polyploidy and high repeat content. We adapted sequence-based whole-genome profiling (WGP™) technology to obtain insight into the polyploidy of the model plant Nicotiana tabacum (tobacco). N. tabacum is assumed to originate from a hybridization event between ancestors of Nicotiana sylvestris and Nicotiana tomentosiformis approximately 200 000 years ago. This resulted in tobacco having a haploid genome size of 4500 million base pairs, approximately four times larger than the related tomato (Solanum lycopersicum) and potato (Solanum tuberosum) genomes. In this study, a physical map containing 9750 contigs of bacterial artificial chromosomes (BACs) was constructed. The mean contig size was 462 kbp, and the calculated genome coverage equaled the estimated tobacco genome size. We used a method for determination of the ancestral origin of the genome by annotation of WGP sequence tags. This assignment agreed with the ancestral annotation available from the tobacco genetic map, and may be used to investigate the evolution of homoeologous genome segments after polyploidization. The map generated is an essential scaffold for the tobacco genome. We propose the combination of WGP physical mapping technology and tag profiling of ancestral lines as a generally applicable method to elucidate the ancestral origin of genome segments of polyploid species. The physical mapping of genes and their origins will enable application of biotechnology to polyploid plants aimed at accelerating and increasing the precision of breeding for abiotic and biotic stress resistance. PMID:23672264

  3. Genome Annotation of Burkholderia sp. SJ98 with Special Focus on Chemotaxis Genes

    PubMed Central

    Kumar, Shailesh; Vikram, Surendra; Raghava, Gajendra Pal Singh

    2013-01-01

    Burkholderia sp. strain SJ98 has the chemotactic activity towards nitroaromatic and chloronitroaromatic compounds. Recently our group published draft genome of strain SJ98. In this study, we further sequence and annotate the genome of stain SJ98 to exploit the potential of this bacterium. We specifically annotate its chemotaxis genes and methyl accepting chemotaxis proteins. Genome of Burkholderia sp. SJ98 was annotated using PGAAP pipeline that predicts 7,268 CDSs, 52 tRNAs and 3 rRNAs. Our analysis based on phylogenetic and comparative genomics suggest that Burkholderia sp. YI23 is closest neighbor of the strain SJ98. The genes involved in the chemotaxis of strain SJ98 were compared with genes of closely related Burkholderia strains (i.e. YI23, CCGE 1001, CCGE 1002, CCGE 1003) and with well characterized bacterium E. coli K12. It was found that strain SJ98 has 37 che genes including 19 methyl accepting chemotaxis proteins that involved in sensing of different attractants. Chemotaxis genes have been found in a cluster along with the flagellar motor proteins. We also developed a web resource that provides comprehensive information on strain SJ98 that includes all analysis data (http://crdd.osdd.net/raghava/genomesrs/burkholderia/). PMID:23940608

  4. Discovery and characterization of chromatin states for systematic annotation of the human genome

    PubMed Central

    Ernst, Jason; Kellis, Manolis

    2010-01-01

    A plethora of epigenetic modifications have been described in the human genome and shown to play diverse roles in gene regulation, cellular differentiation, and the onset of disease. While some modifications have been linked with activity levels of different functional elements, their combinatorial patterns remain unresolved, and their potential for systematic de novo genome annotation remains untapped. In this paper, we systematically discover and characterize recurrent spatially-coherent and biologically-meaningful chromatin mark combinations, or chromatin states, in human T-cells. We describe 51 distinct chromatin states, including promoter-associated, transcription-associated, active intergenic, large-scale repressed and repeat-associated states. Each chromatin state shows specific functional, experimental, conservation, annotation, and sequence-motif enrichments, revealing their distinct candidate biological roles. Overall, our work provides a complementary functional annotation of the human genome revealing the genome-wide locations of diverse classes of epigenetic functions, including previously-unsuspected chromatin states enriched in transcription end sites, distinct repeat families, and disease-SNP-associated states. PMID:20657582

  5. Complete, Annotated Sequence of the Pseudorabies Virus Genome

    PubMed Central

    Klupp, Barbara G.; Hengartner, Christoph J.; Mettenleiter, Thomas C.; Enquist, Lynn W.

    2004-01-01

    We have obtained the complete DNA sequence of pseudorabies virus (PRV), an alphaherpesvirus also known as Aujeszky's disease virus or suid herpesvirus 1, using sequence fragments derived from six different strains (Kaplan, Becker, Rice, Indiana-Funkhauser, NIA-3, and TNL). The assembled PRV genome sequence comprises 143,461 nucleotides. As expected, it matches the predicted gene arrangement, genome size, and restriction enzyme digest patterns. More than 70 open reading frames were identified with homologs in related alphaherpesviruses; none were unique to PRV. RNA polymerase II transcriptional control elements in the PRV genome, including core promoters, splice sites, and polyadenylation sites, were identified with computer prediction programs. The correlation between predicted and experimentally determined transcription start and stop sites was excellent. The transcriptional control architecture is characterized by three key features: core transcription elements shared between genes, yielding divergent transcripts and a large number of coterminal transcripts; bifunctional transcriptional elements, yielding head-to-tail transcripts; and short repetitive sequences that could function as insulators against improperly terminated transcripts. Many of these features are conserved in the alphaherpesvirus subfamily and have important implications for gene array analyses. PMID:14671123

  6. Polymorphism Identification and Improved Genome Annotation of Brassica rapa Through Deep RNA Sequencing

    PubMed Central

    Devisetty, Upendra Kumar; Covington, Michael F.; Tat, An V.; Lekkala, Saradadevi; Maloof, Julin N.

    2014-01-01

    The mapping and functional analysis of quantitative traits in Brassica rapa can be greatly improved with the availability of physically positioned, gene-based genetic markers and accurate genome annotation. In this study, deep transcriptome RNA sequencing (RNA-Seq) of Brassica rapa was undertaken with two objectives: SNP detection and improved transcriptome annotation. We performed SNP detection on two varieties that are parents of a mapping population to aid in development of a marker system for this population and subsequent development of high-resolution genetic map. An improved Brassica rapa transcriptome was constructed to detect novel transcripts and to improve the current genome annotation. This is useful for accurate mRNA abundance and detection of expression QTL (eQTLs) in mapping populations. Deep RNA-Seq of two Brassica rapa genotypes—R500 (var. trilocularis, Yellow Sarson) and IMB211 (a rapid cycling variety)—using eight different tissues (root, internode, leaf, petiole, apical meristem, floral meristem, silique, and seedling) grown across three different environments (growth chamber, greenhouse and field) and under two different treatments (simulated sun and simulated shade) generated 2.3 billion high-quality Illumina reads. A total of 330,995 SNPs were identified in transcribed regions between the two genotypes with an average frequency of one SNP in every 200 bases. The deep RNA-Seq reassembled Brassica rapa transcriptome identified 44,239 protein-coding genes. Compared with current gene models of B. rapa, we detected 3537 novel transcripts, 23,754 gene models had structural modifications, and 3655 annotated proteins changed. Gaps in the current genome assembly of B. rapa are highlighted by our identification of 780 unmapped transcripts. All the SNPs, annotations, and predicted transcripts can be viewed at http://phytonetworks.ucdavis.edu/. PMID:25122667

  7. Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii

    PubMed Central

    2011-01-01

    Background Recent advances in the field of metabolic engineering have been expedited by the availability of genome sequences and metabolic modelling approaches. The complete sequencing of the C. reinhardtii genome has made this unicellular alga a good candidate for metabolic engineering studies; however, the annotation of the relevant genes has not been validated and the much-needed metabolic ORFeome is currently unavailable. We describe our efforts on the functional annotation of the ORF models released by the Joint Genome Institute (JGI), prediction of their subcellular localizations, and experimental verification of their structural annotation at the genome scale. Results We assigned enzymatic functions to the translated JGI ORF models of C. reinhardtii by reciprocal BLAST searches of the putative proteome against the UniProt and AraCyc enzyme databases. The best match for each translated ORF was identified and the EC numbers were transferred onto the ORF models. Enzymatic functional assignment was extended to the paralogs of the ORFs by clustering ORFs using BLASTCLUST. In total, we assigned 911 enzymatic functions, including 886 EC numbers, to 1,427 transcripts. We further annotated the enzymatic ORFs by prediction of their subcellular localization. The majority of the ORFs are predicted to be compartmentalized in the cytosol and chloroplast. We verified the structure of the metabolism-related ORF models by reverse transcription-PCR of the functionally annotated ORFs. Following amplification and cloning, we carried out 454FLX and Sanger sequencing of the ORFs. Based on alignment of the 454FLX reads to the ORF predicted sequences, we obtained more than 90% coverage for more than 80% of the ORFs. In total, 1,087 ORF models were verified by 454 and Sanger sequencing methods. We obtained expression evidence for 98% of the metabolic ORFs in the algal cells grown under constant light in the presence of acetate. Conclusions We functionally annotated approximately 1

  8. SNPedia: a wiki supporting personal genome annotation, interpretation and analysis.

    PubMed

    Cariaso, Michael; Lennon, Greg

    2012-01-01

    SNPedia (http://www.SNPedia.com) is a wiki resource of the functional consequences of human genetic variation as published in peer-reviewed studies. Online since 2006 and freely available for personal use, SNPedia has focused on the medical, phenotypic and genealogical associations of single nucleotide polymorphisms. Entries are formatted to allow associations to be assigned to single genotypes as well as sets of genotypes (genosets). In this article, we discuss the growth of this resource and its use by affiliated software to create personal genome reports. PMID:22140107

  9. Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam

    DOE PAGESBeta

    Chai, Juanjuan; Kora, Guruprasad; Ahn, Tae-Hyuk; Hyatt, Doug; Pan, Chongle

    2014-10-09

    To supply some background, phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes. Our results show a total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accuratemore » comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history. In conclusion, our functional phylogenomics analysis shows divergent functional profiles of taxa and clades. Such function-phylogeny correlation stems from a set of clade-specific cellular functions with low parsimony scores. On the other hand, many cellular functions are sparsely dispersed across many clades with high parsimony scores. These different types of cellular functions have distinct evolutionary patterns reconstructed from the prokaryotic tree.« less

  10. Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam

    SciTech Connect

    Chai, Juanjuan; Kora, Guruprasad; Ahn, Tae-Hyuk; Hyatt, Doug; Pan, Chongle

    2014-10-09

    To supply some background, phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes. Our results show a total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accurate comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history. In conclusion, our functional phylogenomics analysis shows divergent functional profiles of taxa and clades. Such function-phylogeny correlation stems from a set of clade-specific cellular functions with low parsimony scores. On the other hand, many cellular functions are sparsely dispersed across many clades with high parsimony scores. These different types of cellular functions have distinct evolutionary patterns reconstructed from the prokaryotic tree.

  11. Expanded microbial genome coverage and improved protein family annotation in the COG database

    PubMed Central

    Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I.; Koonin, Eugene V.

    2015-01-01

    Microbial genome sequencing projects produce numerous sequences of deduced proteins, only a small fraction of which have been or will ever be studied experimentally. This leaves sequence analysis as the only feasible way to annotate these proteins and assign to them tentative functions. The Clusters of Orthologous Groups of proteins (COGs) database (http://www.ncbi.nlm.nih.gov/COG/), first created in 1997, has been a popular tool for functional annotation. Its success was largely based on (i) its reliance on complete microbial genomes, which allowed reliable assignment of orthologs and paralogs for most genes; (ii) orthology-based approach, which used the function(s) of the characterized member(s) of the protein family (COG) to assign function(s) to the entire set of carefully identified orthologs and describe the range of potential functions when there were more than one; and (iii) careful manual curation of the annotation of the COGs, aimed at detailed prediction of the biological function(s) for each COG while avoiding annotation errors and overprediction. Here we present an update of the COGs, the first since 2003, and a comprehensive revision of the COG annotations and expansion of the genome coverage to include representative complete genomes from all bacterial and archaeal lineages down to the genus level. This re-analysis of the COGs shows that the original COG assignments had an error rate below 0.5% and allows an assessment of the progress in functional genomics in the past 12 years. During this time, functions of many previously uncharacterized COGs have been elucidated and tentative functional assignments of many COGs have been validated, either by targeted experiments or through the use of high-throughput methods. A particularly important development is the assignment of functions to several widespread, conserved proteins many of which turned out to participate in translation, in particular rRNA maturation and tRNA modification. The new version of the

  12. Toward a Functional Annotation of the Human Genome Using Artificial Transcription Factors

    PubMed Central

    Lee, Dong-ki; Park, Jin Woo; Kim, Youn-Jae; Kim, Jiwon; Lee, Yangsoon; Kim, Jeonglim; Kim, Jin-Soo

    2003-01-01

    We have developed a novel, high-throughput approach to collecting randomly perturbed gene-expression profiles from the human genome.A human 293 cell library that stably expresses randomly chosen zinc-finger transcription factors was constructed, and the expression profile of each cell line was obtained using cDNA microarray technology.Gene expression profiles from a total of 132 cell lines were collected and analyzed by (1) a simple clustering method based on expression-profile similarity, and (2) the shortest-path analysis method.These analyses identified a number of gene groups, and further investigation revealed that the genes that were grouped together had close biological relationships.The artificial transcription factor-based random genome perturbation method thus provides a novel functional genomic tool for annotation and classification of genes in the human genome and those of many other organisms. PMID:14656973

  13. Systematic functional genomics resource and annotation for poplar.

    PubMed

    Si, Jingna; Zhao, Xiyang; Zhao, Xinyin; Wu, Rongling

    2015-08-01

    Poplar, as a model species for forestry research, has many excellent characteristics. Studies on functional genes have provided the foundation, at the molecular level, for improving genetic traits and cultivating elite lines. Although studies on functional genes have been performed for many years, large amounts of experimental data remain scattered across various reports and have not been unified via comprehensive statistical analysis. This problem can be addressed by employing bioinformatic methodology and technology to gather and organise data to construct a Poplar Functional Gene Database, containing data on 207 poplar functional genes. As an example, the authors investigated genes of Populus euphratica involved in the response to salt stress. Four small cDNA libraries were constructed and treated with 300 mM NaCl or pure water for 6 and 24 h. Using high-throughput sequencing, they identified conserved and novel miRNAs that were differentially expressed. Target genes were next predicted and detailed functional information derived using the Gene Ontology database and Kyoto Encyclopedia of Genes and Genomes pathway analysis. This information provides a primary visual schema allowing us to understand the dynamics of the regulatory gene network responding to salt stress in Populus. PMID:26243833

  14. Genome-scale phylogenetic function annotation of large and diverse protein families

    PubMed Central

    Engelhardt, Barbara E.; Jordan, Michael I.; Srouji, John R.; Brenner, Steven E.

    2011-01-01

    The Statistical Inference of Function Through Evolutionary Relationships (SIFTER) framework uses a statistical graphical model that applies phylogenetic principles to automate precise protein function prediction. Here we present a revised approach (SIFTER version 2.0) that enables annotations on a genomic scale. SIFTER 2.0 produces equivalently precise predictions compared to the earlier version on a carefully studied family and on a collection of 100 protein families. We have added an approximation method to SIFTER 2.0 and show a 500-fold improvement in speed with minimal impact on prediction results in the functionally diverse sulfotransferase protein family. On the Nudix protein family, previously inaccessible to the SIFTER framework because of the 66 possible molecular functions, SIFTER achieved 47.4% accuracy on experimental data (where BLAST achieved 34.0%). Finally, we used SIFTER to annotate all of the Schizosaccharomyces pombe proteins with experimental functional characterizations, based on annotations from proteins in 46 fungal genomes. SIFTER precisely predicted molecular function for 45.5% of the characterized proteins in this genome, as compared with four current function prediction methods that precisely predicted function for 62.6%, 30.6%, 6.0%, and 5.7% of these proteins. We use both precision-recall curves and ROC analyses to compare these genome-scale predictions across the different methods and to assess performance on different types of applications. SIFTER 2.0 is capable of predicting protein molecular function for large and functionally diverse protein families using an approximate statistical model, enabling phylogenetics-based protein function prediction for genome-wide analyses. The code for SIFTER and protein family data are available at http://sifter.berkeley.edu. PMID:21784873

  15. Sequencing and genome annotation of honey bee microsporidia parasite, Nosema apis and comparative genome analysis with its sympatric congener, N. ceranae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Here we present a draft genome sequence and annotation of the honey bee microsporidian parasite, Nosema apis. We applied the whole-genome shotgun (WGS) sequencing approach to sequence and assemble the genome of N. apis to 22-fold sequence coverage. We predicted 2927 protein-coding genes in the N. ...

  16. A field guide to whole-genome sequencing, assembly and annotation

    PubMed Central

    Ekblom, Robert; Wolf, Jochen B W

    2014-01-01

    Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole-genome sequencing projects. PMID:25553065

  17. Bacillus pumilus SAFR-032 Genome Revisited: Sequence Update and Re-Annotation

    PubMed Central

    Stepanov, Victor G.; Tirumalai, Madhan R.; Montazari, Saied; Checinska, Aleksandra; Venkateswaran, Kasthuri

    2016-01-01

    Bacillus pumilus strain SAFR-032 is a non-pathogenic spore-forming bacterium exhibiting an anomalously high persistence in bactericidal environments. In its dormant state, it is capable of withstanding doses of ultraviolet (UV) radiation or hydrogen peroxide, which are lethal for the vast majority of microorganisms. This unusual resistance profile has made SAFR-032 a reference strain for studies of bacterial spore resistance. The complete genome sequence of B. pumilus SAFR-032 was published in 2007 early in the genomics era. Since then, the SAFR-032 strain has frequently been used as a source of genetic/genomic information that was regarded as representative of the entire B. pumilus species group. Recently, our ongoing studies of conservation of gene distribution patterns in the complete genomes of various B. pumilus strains revealed indications of misassembly in the B. pumilus SAFR-032 genome. Synteny-driven local genome resequencing confirmed that the original SAFR-032 sequence contained assembly errors associated with long sequence repeats. The genome sequence was corrected according to the new findings. In addition, a significantly improved annotation is now available. Gene orders were compared and portions of the genome arrangement were found to be similar in a wide spectrum of Bacillus strains. PMID:27351589

  18. SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals

    PubMed Central

    Damienikan, Aliaksandr U.

    2016-01-01

    The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn’t fit with regulatory information allowed us to correct product and gene names for over 300 loci. PMID:27257541

  19. SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals.

    PubMed

    Nikolaichik, Yevgeny; Damienikan, Aliaksandr U

    2016-01-01

    The majority of bacterial genome annotations are currently automated and based on a 'gene by gene' approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn't fit with regulatory information allowed us to correct product and gene names for over 300 loci. PMID:27257541

  20. Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability

    PubMed Central

    Bitton, Danny A.; Wood, Valerie; Scutt, Paul J.; Grallert, Agnes; Yates, Tim; Smith, Duncan L.; Hagan, Iain M.; Miller, Crispin J.

    2011-01-01

    Genome annotation is a synthesis of computational prediction and experimental evidence. Small genes are notoriously difficult to detect because the patterns used to identify them are often indistinguishable from chance occurrences, leading to an arbitrary cutoff threshold for the length of a protein-coding gene identified solely by in silico analysis. We report a systematic reappraisal of the Schizosaccharomyces pombe genome that ignores thresholds. A complete six-frame translation was compared to a proteome data set, the Pfam domain database, and the genomes of six other fungi. Thirty-nine novel loci were identified. RT-PCR and RNA-Seq confirmed transcription at 38 loci; 33 novel gene structures were delineated by 5′ and 3′ RACE. Expression levels of 14 transcripts fluctuated during meiosis. Translational evidence for 10 genes, evolutionary conservation data supporting 35 predictions, and distinct phenotypes upon ORF deletion (one essential, four slow-growth, two delayed-division phenotypes) suggest that all 39 predictions encode functional proteins. The popularity of S. pombe as a model organism suggests that this augmented annotation will be of interest in diverse areas of molecular and cellular biology, while the generality of the approach suggests widespread applicability to other genomes. PMID:21270388

  1. The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation

    SciTech Connect

    Mavromatis, K; Land, Miriam L; Brettin, Thomas S; Quest, Daniel J; Copeland, A; Clum, Alicia; Goodwin, Lynne A.; Woyke, Tanja; Lapidus, Alla L.; Klenk, Hans-Peter; Cottingham, Robert W; Kyrpides, Nikos C

    2012-01-01

    Background: The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. Methodology/Principal Findings: In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. Conclusion: These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).

  2. Discovery and annotation of small proteins using genomics, proteomics and computational approaches

    SciTech Connect

    Yang, Xiaohan; Tschaplinski, Timothy J.; Hurst, Gregory B.; Jawdy, Sara; Abraham, Paul E.; Lankford, Patricia K.; Adams, Rachel M.; Shah, Manesh B.; Hettich, Robert L.; Lindquist, Erika; Kalluri, Udaya C.; Gunter, Lee E.; Pennacchio, Christa; Tuskan, Gerald A.

    2011-03-02

    Small proteins (10 200 amino acids aa in length) encoded by short open reading frames (sORF) play important regulatory roles in various biological processes, including tumor progression, stress response, flowering, and hormone signaling. However, ab initio discovery of small proteins has been relatively overlooked. Recent advances in deep transcriptome sequencing make it possible to efficiently identify sORFs at the genome level. In this study, we obtained 2.6 million expressed sequence tag (EST) reads from Populus deltoides leaf transcriptome and reconstructed full-length transcripts from the EST sequences. We identified an initial set of 12,852 sORFs encoding proteins of 10 200 aa in length. Three computational approaches were then used to enrich for bona fide protein-coding sORFs from the initial sORF set: (1) codingpotential prediction, (2) evolutionary conservation between P. deltoides and other plant species, and (3) gene family clustering within P. deltoides. As a result, a high-confidence sORF candidate set containing 1469 genes was obtained. Analysis of the protein domains, non-protein-coding RNA motifs, sequence length distribution, and protein mass spectrometry data supported this high-confidence sORF set. In the high-confidence sORF candidate set, known protein domains were identified in 1282 genes (higher-confidence sORF candidate set), out of which 611 genes, designated as highest-confidence candidate sORF set, were supported by proteomics data. Of the 611 highest-confidence candidate sORF genes, 56 were new to the current Populus genome annotation. This study not only demonstrates that there are potential sORF candidates to be annotated in sequenced genomes, but also presents an efficient strategy for discovery of sORFs in species with no genome annotation yet available.

  3. Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779

    PubMed Central

    Tsai, Chia-Hong; Bullard, Blair; Cornish, Adam J.; Harvey, Christopher; Reca, Ida-Barbara; Thornburg, Chelsea; Achawanantakun, Rujira; Buehl, Christopher J.; Campbell, Michael S.; Cavalier, David; Childs, Kevin L.; Clark, Teresa J.; Deshpande, Rahul; Erickson, Erika; Armenia Ferguson, Ann; Handee, Witawas; Kong, Que; Li, Xiaobo; Liu, Bensheng; Lundback, Steven; Peng, Cheng; Roston, Rebecca L.; Sanjaya; Simpson, Jeffrey P.; TerBush, Allan; Warakanont, Jaruswan; Zäuner, Simone; Farre, Eva M.; Hegg, Eric L.; Jiang, Ning; Kuo, Min-Hao; Lu, Yan; Niyogi, Krishna K.; Ohlrogge, John; Osteryoung, Katherine W.; Shachar-Hill, Yair; Sears, Barbara B.; Sun, Yanni; Takahashi, Hideki; Yandell, Mark; Shiu, Shin-Han; Benning, Christoph

    2012-01-01

    Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high-value lipid products. First success in applying reverse genetics by targeted gene replacement makes Nannochloropsis oceanica an attractive model to investigate the cell and molecular biology and biochemistry of this fascinating organism group. Here we present the assembly of the 28.7 Mb genome of N. oceanica CCMP1779. RNA sequencing data from nitrogen-replete and nitrogen-depleted growth conditions support a total of 11,973 genes, of which in addition to automatic annotation some were manually inspected to predict the biochemical repertoire for this organism. Among others, more than 100 genes putatively related to lipid metabolism, 114 predicted transcription factors, and 109 transcriptional regulators were annotated. Comparison of the N. oceanica CCMP1779 gene repertoire with the recently published N. gaditana genome identified 2,649 genes likely specific to N. oceanica CCMP1779. Many of these N. oceanica–specific genes have putative orthologs in other species or are supported by transcriptional evidence. However, because similarity-based annotations are limited, functions of most of these species-specific genes remain unknown. Aside from the genome sequence and its analysis, protocols for the transformation of N. oceanica CCMP1779 are provided. The availability of genomic and transcriptomic data for Nannochloropsis oceanica CCMP1779, along with efficient transformation protocols, provides a blueprint for future detailed gene functional analysis and genetic engineering of Nannochloropsis species by a growing

  4. Algal Functional Annotation Tool from the DOE-UCLA Institute for Genomics and Proteomics

    DOE Data Explorer

    Lopez, David

    The Algal Functional Annotation Tool is a bioinformatics resource to visualize pathway maps, identify enriched biological terms, or convert gene identifiers to elucidate biological function in silico. These types of analysis have been catered to support lists of gene identifiers, such as those coming from transcriptome gene expression analysis. By analyzing the functional annotation of an interesting set of genes, common biological motifs may be elucidated and a first-pass analysis can point further research in the right direction. Currently, the following databases have been parsed, processed, and added to the tool: 1( Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways Database, 2) MetaCyc Encyclopedia of Metabolic Pathways, 3) Panther Pathways Database, 4) Reactome Pathways Database, 5) Gene Ontology, 6) MapMan Ontology, 7) KOG (Eukaryotic Clusters of Orthologous Groups), 5)Pfam, 6) InterPro.

  5. MAKER-P: a tool-kit for the creation, management, and quality control of plant genome annotations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have optimized and extended the widely used annotation-engine MAKER for use on plant genomes. We have benchmarked the resulting software, MAKER-P, using the A. thaliana genome and the TAIR10 gene models. Here we demonstrate the ability of the MAKER-P toolkit to generate de novo repeat databases, ...

  6. GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes.

    PubMed

    Tuggle, Christopher K; Giuffra, Elisabetta; White, Stephen N; Clarke, Laura; Zhou, Huaijun; Ross, Pablo J; Acloque, Hervé; Reecy, James M; Archibald, Alan; Bellone, Rebecca R; Boichard, Michèle; Chamberlain, Amanda; Cheng, Hans; Crooijmans, Richard P M A; Delany, Mary E; Finno, Carrie J; Groenen, Martien A M; Hayes, Ben; Lunney, Joan K; Petersen, Jessica L; Plastow, Graham S; Schmidt, Carl J; Song, Jiuzhou; Watson, Mick

    2016-10-01

    The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO-FAANG) Workshop in Washington, DC on October 7-8, 2015. This consortium is a grass-roots organization formed to advance the annotation of newly assembled genomes of domesticated and non-model organisms (www.faang.org). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org. In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO-FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta-data analysis standards were established. PMID:27453069

  7. Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome.

    PubMed

    Wang, Jia; Chen, Dijun; Lei, Yang; Chang, Ji-Wei; Hao, Bao-Hai; Xing, Feng; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Chen, Ling-Ling

    2014-01-01

    Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/. PMID:24489955

  8. Functional annotation of risk loci identified through genome-wide association studies for prostate cancer

    PubMed Central

    Lu, Yizhen; Zhang, Zheng; Yu, Hongjie; Zheng, S. Lily; Isaacs, William B.; Xu, Jianfeng; Sun, Jielin

    2010-01-01

    Background The majority of established prostate cancer risk-associated Single Nucleotide Polymorphisms (SNPs) identified from genome-wide association studies do not fall into protein coding regions. Therefore, the mechanisms by which these SNPs affect prostate cancer risk remain unclear. Here, we used a series of bioinformatic tools and databases to provide possible molecular insights into the actions of risk SNPs. Methodology/Principal Findings We performed a comprehensive assessment of the potential functional impact of 33 SNPs that were identified and confirmed as associated with PCa risk in previous studies. For these 33 SNPs and additional SNPs in Linkage Disequilibrium (LD) (r2 ≥ 0.5), we first mapped them to genomic functional annotation databases, including the Encyclopedia of DNA Elements (ENCODE), eleven genomic regulatory elements databases defined by the University of California Santa Cruz (UCSC) table browser, and Androgen Receptor (AR) binding sites defined by a ChIP-chip technique. Enrichment analysis was then carried out to assess whether the risk SNP blocks were enriched in the various annotation sets. Risk SNP blocks were significantly enriched over that expected by chance in two annotation sets, including AR binding sites (p=0.003), and FoxA1 binding sites (p=0.05). About one third of the 33 risk SNP blocks are located within AR binding regions. Conclusions/Significance The significant enrichment of risk SNPs in AR binding sites may suggest a potential molecular mechanism for these SNPs in prostate cancer initiation, and provide guidance for future functional studies. PMID:21541972

  9. Snat: a SNP annotation tool for bovine by integrating various sources of genomic information

    PubMed Central

    2011-01-01

    Background Most recently, with maturing of bovine genome sequencing and high throughput SNP genotyping technologies, a large number of significant SNPs associated with economic important traits can be identified by genome-wide association studies (GWAS). To further determine true association findings in GWAS, the common strategy is to sift out most promising SNPs for follow-up replication studies. Hence it is crucial to explore the functional significance of the candidate SNPs in order to screen and select the potential functional ones. To systematically prioritize these statistically significant SNPs and facilitate follow-up replication studies, we developed a bovine SNP annotation tool (Snat) based on a web interface. Results With Snat, various sources of genomic information are integrated and retrieved from several leading online databases, including SNP information from dbSNP, gene information from Entrez Gene, protein features from UniProt, linkage information from AnimalQTLdb, conserved elements from UCSC Genome Browser Database and gene functions from Gene Ontology (GO), KEGG PATHWAY and Online Mendelian Inheritance in Animals (OMIA). Snat provides two different applications, including a CGI-based web utility and a command-line version, to access the integrated database, target any single nucleotide loci of interest and perform multi-level functional annotations. For further validation of the practical significance of our study, SNPs involved in two commercial bovine SNP chips, i.e., the Affymetrix Bovine 10K chip array and the Illumina 50K chip array, have been annotated by Snat, and the corresponding outputs can be directly downloaded from Snat website. Furthermore, a real dataset involving 20 identified SNPs associated with milk yield in our recent GWAS was employed to demonstrate the practical significance of Snat. Conclusions To our best knowledge, Snat is one of first tools focusing on SNP annotation for livestock. Snat confers researchers with a

  10. High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade

    PubMed Central

    2012-01-01

    Background The structural and functional annotation of genomes is now heavily based on data obtained using automated pipeline systems. The key for an accurate structural annotation consists of blending similarities between closely related genomes with biochemical evidence of the genome interpretation. In this work we applied high-throughput proteogenomics to Ruegeria pomeroyi, a member of the Roseobacter clade, an abundant group of marine bacteria, as a seed for the annotation of the whole clade. Results A large dataset of peptides from R. pomeroyi was obtained after searching over 1.1 million MS/MS spectra against a six-frame translated genome database. We identified 2006 polypeptides, of which thirty-four were encoded by open reading frames (ORFs) that had not previously been annotated. From the pool of 'one-hit-wonders', i.e. those ORFs specified by only one peptide detected by tandem mass spectrometry, we could confirm the probable existence of five additional new genes after proving that the corresponding RNAs were transcribed. We also identified the most-N-terminal peptide of 486 polypeptides, of which sixty-four had originally been wrongly annotated. Conclusions By extending these re-annotations to the other thirty-six Roseobacter isolates sequenced to date (twenty different genera), we propose the correction of the assigned start codons of 1082 homologous genes in the clade. In addition, we also report the presence of novel genes within operons encoding determinants of the important tricarboxylic acid cycle, a feature that seems to be characteristic of some Roseobacter genomes. The detection of their corresponding products in large amounts raises the question of their function. Their discoveries point to a possible theory for protein evolution that will rely on high expression of orphans in bacteria: their putative poor efficiency could be counterbalanced by a higher level of expression. Our proteogenomic analysis will increase the reliability of the future

  11. Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes

    PubMed Central

    2012-01-01

    Background Tyrosine-based site-specific recombinases (TBSSRs) are DNA breaking-rejoining enzymes. In bacterial genomes, they play a major role in the comings and goings of mobile genetic elements (MGEs), such as temperate phage genomes, integrated conjugative elements (ICEs) or integron cassettes. TBSSRs are also involved in the segregation of plasmids and chromosomes, the resolution of plasmid dimers and of co-integrates resulting from the replicative transposition of transposons. With the aim of improving the annotation of TBSSR genes in genomic sequences and databases, which so far is far from robust, we built a set of over 1,300 TBSSR protein sequences tagged with their genome of origin. We organized them in families to investigate: i) whether TBSSRs tend to be more conserved within than between classes of MGE types and ii) whether the (sub)families may help in understanding more about the function of TBSSRs associated in tandem or trios on plasmids and chromosomes. Results A total of 67% of the TBSSRs in our set are MGE type specific. We define a new class of actinobacterial transposons, related to Tn554, containing one abnormally long TBSSR and one of typical size, and we further characterize numerous TBSSRs trios present in plasmids and chromosomes of α- and β-proteobacteria. Conclusions The simple in silico procedure described here, which uses a set of reference TBSSRs from defined MGE types, could contribute to greatly improve the annotation of tyrosine-based site-specific recombinases in plasmid, (pro)phage and other integrated MGE genomes. It also reveals TBSSRs families whose distribution among bacterial taxa suggests they mediate lateral gene transfer. PMID:22502997

  12. Ab initio gene identification: prokaryote genome annotation with GeneScan and GLIMMER.

    PubMed

    Aggarwal, Gautam; Ramaswamy, Ramakrishna

    2002-02-01

    We compare the annotation of three complete genomes using the ab initio methods of gene identification GeneScan and GLIMMER. The annotation given in GenBank, the standard against which these are compared, has been made using GeneMark. We find a number of novel genes which are predicted by both methods used here, as well as a number of genes that are predicted by GeneMark, but are not identified by either of the nonconsensus methods that we have used. The three organisms studied here are all prokaryotic species with fairly compact genomes. The Fourier measure forms the basis for an efficient non-consensus method for gene prediction, and the algorithm GeneScan exploits this measure. We have bench-marked this program as well as GLIMMER using 3 complete prokaryotic genomes. An effort has also been made to study the limitations of these techniques for complete genome analysis. GeneScan and GLIMMER are of comparable accuracy insofar as gene-identification is concerned, with sensitivities and specificities typically greater than 0.9. The number of false predictions (both positive and negative) is higher for GeneScan as compared to GLIMMER, but in a significant number of cases, similar results are provided by the two techniques. This suggests that there could be some as-yet unidentified additional genes in these three genomes, and also that some of the putative identifications made hitherto might require re-evaluation. All these cases are discussed in detail. PMID:11927773

  13. PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

    PubMed Central

    2010-01-01

    Background Functional genomic studies involving high-throughput sequencing and tiling array applications, such as ChIP-seq and ChIP-chip, generate large numbers of experimentally-derived signal peaks across the genome under study. In analyzing these loci to determine their potential regulatory functions, areas of signal enrichment must be considered relative to proximal genes and regulatory elements annotated throughout the target genome Regions of chromatin association by transcriptional regulators should be distinguished as individual binding sites in order to enhance downstream analyses, such as the identification of known and novel consensus motifs. Results PeakAnalyzer is a set of high-performance utilities for the automated processing of experimentally-derived peak regions and annotation of genomic loci. The programs can accurately subdivide multimodal regions of signal enrichment into distinct subpeaks corresponding to binding sites or chromatin modifications, retrieve genomic sequences encompassing the computed subpeak summits, and identify positional features of interest such as intersection with exon/intron gene components, proximity to up- or downstream transcriptional start sites and cis-regulatory elements. The software can be configured to run either as a pipeline component for high-throughput analyses, or as a cross-platform desktop application with an intuitive user interface. Conclusions PeakAnalyzer comprises a number of utilities essential for ChIP-seq and ChIP-chip data analysis. High-performance implementations are provided for Unix pipeline integration along with a GUI version for interactive use. Source code in C++ and Java is provided, as are native binaries for Linux, Mac OS X and Windows systems. PMID:20691053

  14. SNP annotation-based whole genomic prediction and selection: an application to feed efficiency and its component traits in pigs.

    PubMed

    Do, D N; Janss, L L G; Jensen, J; Kadarmideen, H N

    2015-05-01

    The study investigated genetic architecture and predictive ability using genomic annotation of residual feed intake (RFI) and its component traits (daily feed intake [DFI], ADG, and back fat [BF]). A total of 1,272 Duroc pigs had both genotypic and phenotypic records, and the records were split into a training (968 pigs) and a validation dataset (304 pigs) by assigning records as before and after January 1, 2012, respectively. SNP were annotated by 14 different classes using Ensembl variant effect prediction. Predictive accuracy and prediction bias were calculated using Bayesian Power LASSO, Bayesian A, B, and Cπ, and genomic BLUP (GBLUP) methods. Predictive accuracy ranged from 0.508 to 0.531, 0.506 to 0.532, 0.276 to 0.357, and 0.308 to 0.362 for DFI, RFI, ADG, and BF, respectively. BayesCπ100.1 increased accuracy slightly compared to the GBLUP model and other methods. The contribution per SNP to total genomic variance was similar among annotated classes across different traits. Predictive performance of SNP classes did not significantly differ from randomized SNP groups. Genomic prediction has accuracy comparable to observed phenotype, and use of genomic prediction can be cost effective by replacing feed intake measurement. Genomic annotation had less impact on predictive accuracy traits considered here but may be different for other traits. It is the first study to provide useful insights into biological classes of SNP driving the whole genomic prediction for complex traits in pigs. PMID:26020301

  15. The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component.

    PubMed

    Cherry, J Michael

    2015-12-01

    An ontology is a highly structured form of controlled vocabulary. Each entry in the ontology is commonly called a term. These terms are used when talking about an annotation. However, each term has a definition that, like the definition of a word found within a dictionary, provides the complete usage and detailed explanation of the term. It is critical to consult a term's definition because the distinction between terms can be subtle. The use of ontologies in biology started as a way of unifying communication between scientific communities and to provide a standard dictionary for different topics, including molecular functions, biological processes, mutant phenotypes, chemical properties and structures. The creation of ontology terms and their definitions often requires debate to reach agreement but the result has been a unified descriptive language used to communicate knowledge. In addition to terms and definitions, ontologies require a relationship used to define the type of connection between terms. In an ontology, a term can have more than one parent term, the term above it in an ontology, as well as more than one child, the term below it in the ontology. Many ontologies are used to construct annotations in the Saccharomyces Genome Database (SGD), as in all modern biological databases; however, Gene Ontology (GO), a descriptive system used to categorize gene function, is the most extensively used ontology in SGD annotations. Examples included in this protocol illustrate the structure and features of this ontology. PMID:26631125

  16. PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences.

    PubMed

    Elnitski, Laura; Riemer, Cathy; Petrykowska, Hanna; Florea, Liliana; Schwartz, Scott; Miller, Webb; Hardison, Ross

    2002-12-01

    Sequence conservation between species is useful both for locating coding regions of genes and for identifying functional noncoding segments. Hence interspecies alignment of genomic sequences is an important computational technique. However, its utility is limited without extensive annotation. We describe a suite of software tools, PipTools, and related programs that facilitate the annotation of genes and putative regulatory elements in pairwise alignments. The alignment server PipMaker uses the output of these tools to display detailed information needed to interpret alignments. These programs are provided in a portable format for use on common desktop computers and both the toolkit and the PipMaker server can be found at our Web site (http://bio.cse.psu.edu/). We illustrate the utility of the toolkit using annotation of a pairwise comparison of the mouse MHC class II and class III regions with orthologous human sequences and subsequently identify conserved, noncoding sequences that are DNase I hypersensitive sites in chromatin of mouse cells. PMID:12504859

  17. The de novo genome assembly and annotation of a female domestic dromedary of North African origin.

    PubMed

    Fitak, Robert R; Mohandesan, Elmira; Corander, Jukka; Burger, Pamela A

    2016-01-01

    The single-humped dromedary (Camelus dromedarius) is the most numerous and widespread of domestic camel species and is a significant source of meat, milk, wool, transportation and sport for millions of people. Dromedaries are particularly well adapted to hot, desert conditions and harbour a variety of biological and physiological characteristics with evolutionary, economic and medical importance. To understand the genetic basis of these traits, an extensive resource of genomic variation is required. In this study, we assembled at 65× coverage, a 2.06 Gb draft genome of a female dromedary whose ancestry can be traced to an isolated population from the Canary Islands. We annotated 21 167 protein-coding genes and estimated ~33.7% of the genome to be repetitive. A comparison with the recently published draft genome of an Arabian dromedary resulted in 1.91 Gb of aligned sequence with a divergence of 0.095%. An evaluation of our genome with the reference revealed that our assembly contains more error-free bases (91.2%) and fewer scaffolding errors. We identified ~1.4 million single-nucleotide polymorphisms with a mean density of 0.71 × 10(-3) per base. An analysis of demographic history indicated that changes in effective population size corresponded with recent glacial epochs. Our de novo assembly provides a useful resource of genomic variation for future studies of the camel's adaptations to arid environments and economically important traits. Furthermore, these results suggest that draft genome assemblies constructed with only two differently sized sequencing libraries can be comparable to those sequenced using additional library sizes, highlighting that additional resources might be better placed in technologies alternative to short-read sequencing to physically anchor scaffolds to genome maps. PMID:26178449

  18. Integrative annotation of variants from 1092 humans: application to cancer genomics.

    PubMed

    Khurana, Ekta; Fu, Yao; Colonna, Vincenza; Mu, Xinmeng Jasmine; Kang, Hyun Min; Lappalainen, Tuuli; Sboner, Andrea; Lochovsky, Lucas; Chen, Jieming; Harmanci, Arif; Das, Jishnu; Abyzov, Alexej; Balasubramanian, Suganthi; Beal, Kathryn; Chakravarty, Dimple; Challis, Daniel; Chen, Yuan; Clarke, Declan; Clarke, Laura; Cunningham, Fiona; Evani, Uday S; Flicek, Paul; Fragoza, Robert; Garrison, Erik; Gibbs, Richard; Gümüs, Zeynep H; Herrero, Javier; Kitabayashi, Naoki; Kong, Yong; Lage, Kasper; Liluashvili, Vaja; Lipkin, Steven M; MacArthur, Daniel G; Marth, Gabor; Muzny, Donna; Pers, Tune H; Ritchie, Graham R S; Rosenfeld, Jeffrey A; Sisu, Cristina; Wei, Xiaomu; Wilson, Michael; Xue, Yali; Yu, Fuli; Dermitzakis, Emmanouil T; Yu, Haiyuan; Rubin, Mark A; Tyler-Smith, Chris; Gerstein, Mark

    2013-10-01

    Interpreting variants, especially noncoding ones, in the increasing number of personal genomes is challenging. We used patterns of polymorphisms in functionally annotated regions in 1092 humans to identify deleterious variants; then we experimentally validated candidates. We analyzed both coding and noncoding regions, with the former corroborating the latter. We found regions particularly sensitive to mutations ("ultrasensitive") and variants that are disruptive because of mechanistic effects on transcription-factor binding (that is, "motif-breakers"). We also found variants in regions with higher network centrality tend to be deleterious. Insertions and deletions followed a similar pattern to single-nucleotide variants, with some notable exceptions (e.g., certain deletions and enhancers). On the basis of these patterns, we developed a computational tool (FunSeq), whose application to ~90 cancer genomes reveals nearly a hundred candidate noncoding drivers. PMID:24092746

  19. New local potential useful for genome annotation and 3D modeling

    SciTech Connect

    Chandonia, John-Marc; Cohen, Fred E.

    2003-07-17

    A new potential energy function representing the conformational preferences of sequentially local regions of a protein backbone is presented. This potential is derived from secondary structure probabilities such as those produced by neural network-based prediction methods. The potential is applied to the problem of remote homolog identification, in combination with a distance dependent inter-residue potential and position-based scoring matrices. This fold recognition jury is implemented in a Java application called JThread. These methods are benchmarked on several test sets, including one released entirely after development and parameterization of JThread. In benchmark tests to identify known folds structurally similar (but not identical) to the native structure of a sequence, JThread performs significantly better than PSI-BLAST, with 10 percent more structures correctly identified as the most likely structural match in a fold library, and 20 percent more structures correctly narrowed down to a set of five possible candidates. JThread also significantly improves the average sequence alignment accuracy, from 53 percent to 62 percent of residues correctly aligned. Reliable fold assignments and alignments are identified, making the method useful for genome annotation. JThread is applied to predicted open reading frames (ORFs) from the genomes of Mycoplasma genitalium and Drosophila melanogaster, identifying 20 new structural annotations in the former and 801 in the latter.

  20. DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool

    PubMed Central

    Motion, Graham B.; Howden, Andrew J. M.; Huitema, Edgar; Jones, Susan

    2015-01-01

    There are currently 151 plants with draft genomes available but levels of functional annotation for putative protein products are low. Therefore, accurate computational predictions are essential to annotate genomes in the first instance, and to provide focus for the more costly and time consuming functional assays that follow. DNA-binding proteins are an important class of proteins that require annotation, but current computational methods are not applicable for genome wide predictions in plant species. Here, we explore the use of species and lineage specific models for the prediction of DNA-binding proteins in plants. We show that a species specific support vector machine model based on Arabidopsis sequence data is more accurate (accuracy 81%) than a generic model (74%), and based on this we develop a plant specific model for predicting DNA-binding proteins. We apply this model to the tomato proteome and demonstrate its ability to perform accurate high-throughput prediction of DNA-binding proteins. In doing so, we have annotated 36 currently uncharacterised proteins by assigning a putative DNA-binding function. Our model is publically available and we propose it be used in combination with existing tools to help increase annotation levels of DNA-binding proteins encoded in plant genomes. PMID:26304539

  1. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.

    PubMed

    Plomion, Christophe; Aury, Jean-Marc; Amselem, Joëlle; Alaeitabar, Tina; Barbe, Valérie; Belser, Caroline; Bergès, Hélène; Bodénès, Catherine; Boudet, Nathalie; Boury, Christophe; Canaguier, Aurélie; Couloux, Arnaud; Da Silva, Corinne; Duplessis, Sébastien; Ehrenmann, François; Estrada-Mairey, Barbara; Fouteau, Stéphanie; Francillonne, Nicolas; Gaspin, Christine; Guichard, Cécile; Klopp, Christophe; Labadie, Karine; Lalanne, Céline; Le Clainche, Isabelle; Leplé, Jean-Charles; Le Provost, Grégoire; Leroy, Thibault; Lesur, Isabelle; Martin, Francis; Mercier, Jonathan; Michotey, Célia; Murat, Florent; Salin, Franck; Steinbach, Delphine; Faivre-Rampant, Patricia; Wincker, Patrick; Salse, Jérôme; Quesneville, Hadi; Kremer, Antoine

    2016-01-01

    The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17,910 scaffolds (>2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome. PMID:25944057

  2. Differential annotation of tRNA genes with anticodon CAT in bacterial genomes

    PubMed Central

    Silva, Francisco J.; Belda, Eugeni; Talens, Santiago E.

    2006-01-01

    We have developed three strategies to discriminate among the three types of tRNA genes with anticodon CAT (tRNAIle, elongator tRNAMet and initiator tRNAfMet) in bacterial genomes. With these strategies, we have classified the tRNA genes from 234 bacterial and several organellar genomes. These sequences, in an aligned or unaligned format, may be used for the identification and annotation of tRNA (CAT) genes in other genomes. The first strategy is based on the position of the problem sequences in a phenogram (a tree-like network), the second on the minimum average number of differences against the tRNA sequences of the three types and the third on the search for the highest score value against the profiles of the three types of tRNA genes. The species with the maximum number of tRNAfMet and tRNAMet was Photobacterium profundum, whereas the genome of one Escherichia coli strain presented the maximum number of tRNAIle (CAT) genes. This last tRNA gene and tilS, encoding an RNA-modifying enzyme, are not essential in bacteria. The acquisition of a tRNAIle (TAT) gene by Mycoplasma mobile has led to the loss of both the tRNAIle (CAT) and the tilS genes. The new tRNA has appropriated the function of decoding AUA codons. PMID:17071718

  3. Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies

    PubMed Central

    Wang, Qian; He, Beixin Julie; Zhao, Hongyu

    2016-01-01

    Extensive efforts have been made to understand genomic function through both experimental and computational approaches, yet proper annotation still remains challenging, especially in non-coding regions. In this manuscript, we introduce GenoSkyline, an unsupervised learning framework to predict tissue-specific functional regions through integrating high-throughput epigenetic annotations. GenoSkyline successfully identified a variety of non-coding regulatory machinery including enhancers, regulatory miRNA, and hypomethylated transposable elements in extensive case studies. Integrative analysis of GenoSkyline annotations and results from genome-wide association studies (GWAS) led to novel biological insights on the etiologies of a number of human complex traits. We also explored using tissue-specific functional annotations to prioritize GWAS signals and predict relevant tissue types for each risk locus. Brain and blood-specific annotations led to better prioritization performance for schizophrenia than standard GWAS p-values and non-tissue-specific annotations. As for coronary artery disease, heart-specific functional regions was highly enriched of GWAS signals, but previously identified risk loci were found to be most functional in other tissues, suggesting a substantial proportion of still undetected heart-related loci. In summary, GenoSkyline annotations can guide genetic studies at multiple resolutions and provide valuable insights in understanding complex diseases. GenoSkyline is available at http://genocanyon.med.yale.edu/GenoSkyline. PMID:27058395

  4. Discovery and annotation of small proteins using genomics, proteomics, and computational approaches

    SciTech Connect

    Yang, Xiaohan; Tschaplinski, Timothy J; Hurst, Gregory {Greg} B; Jawdy, Sara; Abraham, Paul E; Lankford, Patricia K; Adams, Rachel M; Shah, Manesh B; Hettich, Robert {Bob} L; Kalluri, Udaya C; Gunter, Lee E; Pennacchio, Christa; Tuskan, Gerald A

    2011-01-01

    Small proteins (10 200 amino acids (AA) in length) encoded by short open reading frames (sORF) play important regulatory roles in various biological processes, including tumor progression, stress response, flowering and hormone signaling. However, ab initio discovery of small proteins has been relatively overlooked. Recent advances in deep transcriptome sequencing make it possible to efficiently identify sORFs at the genome level. In this study, we obtained ~2.6 million expressed sequence tag (EST) reads from Populus deltoides leaf transcriptome and reconstructed full-length transcripts from the EST sequences. We identified an initial set of 12,852 sORFs encoding proteins of 10 200 AA in length. Three computational approaches were then used to enrich for bona fide protein-coding sORFs from the initial sORF set: 1) coding-potential prediction, 2) evolutionary conservation between P. deltoides and other plant species, and 3) gene family clustering within P. deltoides. As a result, a high-confidence sORF candidate set containing 1,469 genes was obtained. Analysis of the protein domains, non-protein-coding RNA motifs, sequence length distribution, and protein mass spectrometry data supported this high-confidence sORF set. In the high-confidence sORF candidate set, known protein domains were identified in 1,282 genes (higher-confidence sORF candidate set), out of which 611 genes, designated as highest-confidence candidate sORF set, were also supported by proteomics data. This study not only demonstrates that there are potential sORF candidates to be annotated in sequenced genomes, but also presents an efficient strategy for discovery of sORFs in species with no genome annotation yet available.

  5. Semantic Assembly and Annotation of Draft RNAseq Transcripts without a Reference Genome

    PubMed Central

    Ptitsyn, Andrey; Temanni, Ramzi; Bouchard, Christelle; Anderson, Peter A. V.

    2015-01-01

    Transcriptomes are one of the first sources of high-throughput genomic data that have benefitted from the introduction of Next-Gen Sequencing. As sequencing technology becomes more accessible, transcriptome sequencing is applicable to multiple organisms for which genome sequences are unavailable. Currently all methods for de novo assembly are based on the concept of matching the nucleotide context overlapping between short fragments-reads. However, even short reads may still contain biologically relevant information which can be used as hints in guiding the assembly process. We propose a computational workflow for the reconstruction and functional annotation of expressed gene transcripts that does not require a reference genome sequence and can be tolerant to low coverage, high error rates and other issues that often lead to poor results of de novo assembly in studies of non-model organisms. We start with either raw sequences or the output of a context-based de novo transcriptome assembly. Instead of mapping reads to a reference genome or creating a completely unsupervised clustering of reads, we assemble the unknown transcriptome using nearest homologs from a public database as seeds. We consider even distant relations, indirectly linking protein-coding fragments to entire gene families in multiple distantly related genomes. The intended application of the proposed method is an additional step of semantic (based on relations between protein-coding fragments) scaffolding following traditional (i.e. based on sequence overlap) de novo assembly. The method we developed was effective in analysis of the jellyfish Cyanea capillata transcriptome and may be applicable in other studies of gene expression in species lacking a high quality reference genome sequence. Our algorithms are implemented in C and designed for parallel computation using a high-performance computer. The software is available free of charge via an open source license. PMID:26393794

  6. MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations1[W][OPEN

    PubMed Central

    Campbell, Michael S.; Law, MeiYee; Holt, Carson; Stein, Joshua C.; Moghe, Gaurav D.; Hufnagel, David E.; Lei, Jikai; Achawanantakun, Rujira; Jiao, Dian; Lawrence, Carolyn J.; Ware, Doreen; Shiu, Shin-Han; Childs, Kevin L.; Sun, Yanni; Jiang, Ning; Yandell, Mark

    2014-01-01

    We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. New features include better parallelization for large repeat-rich plant genomes, noncoding RNA annotation capabilities, and support for pseudogene identification. We have benchmarked the resulting software tool kit, MAKER-P, using the Arabidopsis (Arabidopsis thaliana) and maize (Zea mays) genomes. Here, we demonstrate the ability of the MAKER-P tool kit to automatically update, extend, and revise the Arabidopsis annotations in light of newly available data and to annotate pseudogenes and noncoding RNAs absent from The Arabidopsis Informatics Resource 10 build. Our results demonstrate that MAKER-P can be used to manage and improve the annotations of even Arabidopsis, perhaps the best-annotated plant genome. We have also installed and benchmarked MAKER-P on the Texas Advanced Computing Center. We show that this public resource can de novo annotate the entire Arabidopsis and maize genomes in less than 3 h and produce annotations of comparable quality to those of the current The Arabidopsis Information Resource 10 and maize V2 annotation builds. PMID:24306534

  7. Genome Wide Re-Annotation of Caldicellulosiruptor saccharolyticus with New Insights into Genes Involved in Biomass Degradation and Hydrogen Production

    PubMed Central

    Chowdhary, Nupoor; Selvaraj, Ashok; KrishnaKumaar, Lakshmi; Kumar, Gopal Ramesh

    2015-01-01

    Caldicellulosiruptor saccharolyticus has proven itself to be an excellent candidate for biological hydrogen (H2) production, but still it has major drawbacks like sensitivity to high osmotic pressure and low volumetric H2 productivity, which should be considered before it can be used industrially. A whole genome re-annotation work has been carried out as an attempt to update the incomplete genome information that causes gap in the knowledge especially in the area of metabolic engineering, to improve the H2 producing capabilities of C. saccharolyticus. Whole genome re-annotation was performed through manual means for 2,682 Coding Sequences (CDSs). Bioinformatics tools based on sequence similarity, motif search, phylogenetic analysis and fold recognition were employed for re-annotation. Our methodology could successfully add functions for 409 hypothetical proteins (HPs), 46 proteins previously annotated as putative and assigned more accurate functions for the known protein sequences. Homology based gene annotation has been used as a standard method for assigning function to novel proteins, but over the past few years many non-homology based methods such as genomic context approaches for protein function prediction have been developed. Using non-homology based functional prediction methods, we were able to assign cellular processes or physical complexes for 249 hypothetical sequences. Our re-annotation pipeline highlights the addition of 231 new CDSs generated from MicroScope Platform, to the original genome with functional prediction for 49 of them. The re-annotation of HPs and new CDSs is stored in the relational database that is available on the MicroScope web-based platform. In parallel, a comparative genome analyses were performed among the members of genus Caldicellulosiruptor to understand the function and evolutionary processes. Further, with results from integrated re-annotation studies (homology and genomic context approach), we strongly suggest that Csac

  8. A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context

    PubMed Central

    Edwards, Martin T.; Rison, Stuart C. G.; Stoker, Neil G.; Wernisch, Lorenz

    2005-01-01

    An important step in understanding the regulation of a prokaryotic genome is the generation of its transcription unit map. The current strongest operon predictor depends on the distributions of intergenic distances (IGD) separating adjacent genes within and between operons. Unfortunately, experimental data on these distance distributions are limited to Escherichia coli and Bacillus subtilis. We suggest a new graph algorithmic approach based on comparative genomics to identify clusters of conserved genes independent of IGD and conservation of gene order. As a consequence, distance distributions of operon pairs for any arbitrary prokaryotic genome can be inferred. For E.coli, the algorithm predicts 854 conserved adjacent pairs with a precision of 85%. The IGD distribution for these pairs is virtually identical to the E.coli operon pair distribution. Statistical analysis of the predicted pair IGD distribution allows estimation of a genome-specific operon IGD cut-off, obviating the requirement for a training set in IGD-based operon prediction. We apply the method to a representative set of eight genomes, and show that these genome-specific IGD distributions differ considerably from each other and from the distribution in E.coli. PMID:15942028

  9. PeerGAD: a peer-review-based and community-centric web application for viewing and annotating prokaryotic genome sequences

    PubMed Central

    D’Ascenzo, Mark D.; Collmer, Alan; Martin, Gregory B.

    2004-01-01

    PeerGAD is a web-based database-driven application that allows community-wide peer-reviewed annotation of prokaryotic genome sequences. The application was developed to support the annotation of the Pseudomonas syringae pv. tomato strain DC3000 genome sequence and is easily portable to other genome sequence annotation projects. PeerGAD incorporates several innovative design and operation features and accepts annotations pertaining to gene naming, role classification, gene translation and annotation derivation. The annotator tool in PeerGAD is built around a genome browser that offers users the ability to search and navigate the genome sequence. Because the application encourages annotation of the genome sequence directly by researchers and relies on peer review, it circumvents the need for an annotation curator while providing added value to the annotation data. Support for the Gene Ontology™ vocabulary, a structured and controlled vocabulary used in classification of gene roles, is emphasized throughout the system. Here we present the underlying concepts integral to the functionality of PeerGAD. PMID:15184545

  10. Rapid Virulence Annotation (RVA): Identification of virulence factors using a bacterial genome library and multiple invertebrate hosts

    PubMed Central

    Waterfield, Nicholas R.; Sanchez-Contreras, Maria; Eleftherianos, Ioannis; Dowling, Andrea; Yang, Guowei; Wilkinson, Paul; Parkhill, Julian; Thomson, Nicholas; Reynolds, Stuart E.; Bode, Helge B.; Dorus, Steven; ffrench-Constant, Richard H.

    2008-01-01

    Current sequence databases now contain numerous whole genome sequences of pathogenic bacteria. However, many of the predicted genes lack any functional annotation. We describe an assumption-free approach, Rapid Virulence Annotation (RVA), for the high-throughput parallel screening of genomic libraries against four different taxa: insects, nematodes, amoeba, and mammalian macrophages. These hosts represent different aspects of both the vertebrate and invertebrate immune system. Here, we apply RVA to the emerging human pathogen Photorhabdus asymbiotica using “gain of toxicity” assays of recombinant Escherichia coli clones. We describe a wealth of potential virulence loci and attribute biological function to several putative genomic islands, which may then be further characterized using conventional molecular techniques. The application of RVA to other pathogen genomes promises to ascribe biological function to otherwise uncharacterized virulence genes. PMID:18838673

  11. MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data.

    PubMed

    Schmid, Christoph D; Sengstag, Thierry; Bucher, Philipp; Delorenzi, Mauro

    2007-07-01

    A recurring task in the analysis of mass genome annotation data from high-throughput technologies is the identification of peaks or clusters in a noisy signal profile. Examples of such applications are the definition of promoters on the basis of transcription start site profiles, the mapping of transcription factor binding sites based on ChIP-chip data and the identification of quantitative trait loci (QTL) from whole genome SNP profiles. Input to such an analysis is a set of genome coordinates associated with counts or intensities. The output consists of a discrete number of peaks with respective volumes, extensions and center positions. We have developed for this purpose a flexible one-dimensional clustering tool, called MADAP, which we make available as a web server and as standalone program. A set of parameters enables the user to customize the procedure to a specific problem. The web server, which returns results in textual and graphical form, is useful for small to medium-scale applications, as well as for evaluation and parameter tuning in view of large-scale applications, requiring a local installation. The program written in C++ can be freely downloaded from ftp://ftp.epd.unil.ch/pub/software/unix/madap. The MADAP web server can be accessed at http://www.isrec.isb-sib.ch/madap/. PMID:17526516

  12. AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences

    PubMed Central

    Grau, Jan; Reschke, Maik; Erkes, Annett; Streubel, Jana; Morgan, Richard D.; Wilson, Geoffrey G.; Koebnik, Ralf; Boch, Jens

    2016-01-01

    Transcription activator-like effectors (TALEs) are virulence factors, produced by the bacterial plant-pathogen Xanthomonas, that function as gene activators inside plant cells. Although the contribution of individual TALEs to infectivity has been shown, the specific roles of most TALEs, and the overall TALE diversity in Xanthomonas spp. is not known. TALEs possess a highly repetitive DNA-binding domain, which is notoriously difficult to sequence. Here, we describe an improved method for characterizing TALE genes by the use of PacBio sequencing. We present ‘AnnoTALE’, a suite of applications for the analysis and annotation of TALE genes from Xanthomonas genomes, and for grouping similar TALEs into classes. Based on these classes, we propose a unified nomenclature for Xanthomonas TALEs that reveals similarities pointing to related functionalities. This new classification enables us to compare related TALEs and to identify base substitutions responsible for the evolution of TALE specificities. PMID:26876161

  13. Quantitative frame analysis and the annotation of GC-rich (and other) prokaryotic genomes. An application to Anaeromyxobacter dehalogenans

    PubMed Central

    Oden, Steve; Brocchieri, Luciano

    2015-01-01

    Motivation: Graphical representations of contrasts in GC usage among codon frame positions (frame analysis) provide evidence of genes missing from the annotations of prokaryotic genomes of high GC content but the qualitative approach of visual frame analysis prevents its applicability on a genomic scale. Results: We developed two quantitative methods for the identification and statistical characterization in sequence regions of three-base periodicity (hits) associated with open reading frame structures. The methods were implemented in the N-Profile Analysis Computational Tool (NPACT), which highlights in graphical representations inconsistencies between newly identified ORFs and pre-existing annotations of coding-regions. We applied the NPACT procedures to two recently annotated strains of the deltaproteobacterium Anaeromyxobacter dehalogenans, identifying in both genomes numerous conserved ORFs not included in the published annotation of coding regions. Availability and implementation: NPACT is available as a web-based service and for download at http://genome.ufl.edu/npact. Contact: lucianob@ufl.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26048600

  14. A kingdom-specific protein domain HMM library for improved annotation of fungal genomes

    PubMed Central

    Alam, Intikhab; Hubbard, Simon J; Oliver, Stephen G; Rattray, Magnus

    2007-01-01

    Background Pfam is a general-purpose database of protein domain alignments and profile Hidden Markov Models (HMMs), which is very popular for the annotation of sequence data produced by genome sequencing projects. Pfam provides models that are often very general in terms of the taxa that they cover and it has previously been suggested that such general models may lack some of the specificity or selectivity that would be provided by kingdom-specific models. Results Here we present a general approach to create domain libraries of HMMs for sub-taxa of a kingdom. Taking fungal species as an example, we construct a domain library of HMMs (called Fungal Pfam or FPfam) using sequences from 30 genomes, consisting of 24 species from the ascomycetes group and two basidiomycetes, Ustilago maydis, a fungal pathogen of maize, and the white rot fungus Phanerochaete chrysosporium. In addition, we include the Microsporidion Encephalitozoon cuniculi, an obligate intracellular parasite, and two non-fungal species, the oomycetes Phytophthora sojae and Phytophthora ramorum, both plant pathogens. We evaluate the performance in terms of coverage against the original 30 genomes used in training FPfam and against five more recently sequenced fungal genomes that can be considered as an independent test set. We show that kingdom-specific models such as FPfam can find instances of both novel and well characterized domains, increases overall coverage and detects more domains per sequence with typically higher bitscores than Pfam for the same domain families. An evaluation of the effect of changing E-values on the coverage shows that the performance of FPfam is consistent over the range of E-values applied. Conclusion Kingdom-specific models are shown to provide improved coverage. However, as the models become more specific, some sequences found by Pfam may be missed by the models in FPfam and some of the families represented in the test set are not present in FPfam. Therefore, we recommend

  15. The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation

    PubMed Central

    Singh, Meghna; Bhartiya, Deeksha; Maini, Jayant; Sharma, Meenakshi; Singh, Angom Ramcharan; Kadarkaraisamy, Subburaj; Rana, Rajiv; Sabharwal, Ankit; Nanda, Srishti; Ramachandran, Aravindhakshan; Mittal, Ashish; Kapoor, Shruti; Sehgal, Paras; Asad, Zainab; Kaushik, Kriti; Vellarikkal, Shamsudheen Karuthedath; Jagga, Divya; Muthuswami, Muthulakshmi; Chauhan, Rajendra K.; Leonard, Elvin; Priyadarshini, Ruby; Halimani, Mahantappa; Malhotra, Sunny; Patowary, Ashok; Vishwakarma, Harinder; Joshi, Prateek; Bhardwaj, Vivek; Bhaumik, Arijit; Bhatt, Bharat; Jha, Aamod; Kumar, Aalok; Budakoti, Prerna; Lalwani, Mukesh Kumar; Meli, Rajeshwari; Jalali, Saakshi; Joshi, Kandarp; Pal, Koustav; Dhiman, Heena; Laddha, Saurabh V.; Jadhav, Vaibhav; Singh, Naresh; Pandey, Vikas; Sachidanandan, Chetana; Ekker, Stephen C.; Klee, Eric W.; Scaria, Vinod; Sivasubbu, Sridhar

    2014-01-01

    A large repertoire of gene-centric data has been generated in the field of zebrafish biology. Although the bulk of these data are available in the public domain, most of them are not readily accessible or available in nonstandard formats. One major challenge is to unify and integrate these widely scattered data sources. We tested the hypothesis that active community participation could be a viable option to address this challenge. We present here our approach to create standards for assimilation and sharing of information and a system of open standards for database intercommunication. We have attempted to address this challenge by creating a community-centric solution for zebrafish gene annotation. The Zebrafish GenomeWiki is a ‘wiki’-based resource, which aims to provide an altruistic shared environment for collective annotation of the zebrafish genes. The Zebrafish GenomeWiki has features that enable users to comment, annotate, edit and rate this gene-centric information. The credits for contributions can be tracked through a transparent microattribution system. In contrast to other wikis, the Zebrafish GenomeWiki is a ‘structured wiki’ or rather a ‘semantic wiki’. The Zebrafish GenomeWiki implements a semantically linked data structure, which in the future would be amenable to semantic search. Database URL: http://genome.igib.res.in/twiki PMID:24578356

  16. Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome

    PubMed Central

    Tsai, Hsin Y.; Robledo, Diego; Lowe, Natalie R.; Bekaert, Michael; Taggart, John B.; Bron, James E.; Houston, Ross D.

    2016-01-01

    High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterization of the recombination landscape of a species’ genome. Genomic resources for Atlantic salmon (Salmo salar) include a well-assembled reference genome, and high density single nucleotide polymorphism (SNP) arrays. Our aim was to create a high density linkage map, and to align it with the reference genome assembly. Over 96,000 SNPs were mapped and ordered on the 29 salmon linkage groups using a pedigreed population comprising 622 fish from 60 nuclear families, all genotyped with the ‘ssalar01’ high density SNP array. The number of SNPs per group showed a high positive correlation with physical chromosome length (r = 0.95). While the order of markers on the genetic and physical maps was generally consistent, areas of discrepancy were identified. Approximately 6.5% of the previously unmapped reference genome sequence was assigned to chromosomes using the linkage map. Male recombination rate was lower than females across the vast majority of the genome, but with a notable peak in subtelomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorized according to their predicted function, including annotation of ∼2500 putative nonsynonymous variants. The highest density SNP linkage map for any salmonid species has been created, annotated, and integrated with the Atlantic salmon reference genome assembly. This map highlights the marked heterochiasmy of salmon, and provides a useful resource for salmonid genetics and genomics research. PMID:27194803

  17. Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome.

    PubMed

    Tsai, Hsin Y; Robledo, Diego; Lowe, Natalie R; Bekaert, Michael; Taggart, John B; Bron, James E; Houston, Ross D

    2016-01-01

    High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterization of the recombination landscape of a species' genome. Genomic resources for Atlantic salmon (Salmo salar) include a well-assembled reference genome, and high density single nucleotide polymorphism (SNP) arrays. Our aim was to create a high density linkage map, and to align it with the reference genome assembly. Over 96,000 SNPs were mapped and ordered on the 29 salmon linkage groups using a pedigreed population comprising 622 fish from 60 nuclear families, all genotyped with the 'ssalar01' high density SNP array. The number of SNPs per group showed a high positive correlation with physical chromosome length (r = 0.95). While the order of markers on the genetic and physical maps was generally consistent, areas of discrepancy were identified. Approximately 6.5% of the previously unmapped reference genome sequence was assigned to chromosomes using the linkage map. Male recombination rate was lower than females across the vast majority of the genome, but with a notable peak in subtelomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorized according to their predicted function, including annotation of ∼2500 putative nonsynonymous variants. The highest density SNP linkage map for any salmonid species has been created, annotated, and integrated with the Atlantic salmon reference genome assembly. This map highlights the marked heterochiasmy of salmon, and provides a useful resource for salmonid genetics and genomics research. PMID:27194803

  18. Use of Modern Chemical Protein Synthesis and Advanced Fluorescent Assay Techniques to Experimentally Validate the Functional Annotation of Microbial Genomes

    SciTech Connect

    Kent, Stephen

    2012-07-20

    The objective of this research program was to prototype methods for the chemical synthesis of predicted protein molecules in annotated microbial genomes. High throughput chemical methods were to be used to make large numbers of predicted proteins and protein domains, based on microbial genome sequences. Microscale chemical synthesis methods for the parallel preparation of peptide-thioester building blocks were developed; these peptide segments are used for the parallel chemical synthesis of proteins and protein domains. Ultimately, it is envisaged that these synthetic molecules would be ‘printed’ in spatially addressable arrays. The unique ability of total synthesis to precision label protein molecules with dyes and with chemical or biochemical ‘tags’ can be used to facilitate novel assay technologies adapted from state-of-the art single molecule fluorescence detection techniques. In the future, in conjunction with modern laboratory automation this integrated set of techniques will enable high throughput experimental validation of the functional annotation of microbial genomes.

  19. Next-Generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011

    PubMed Central

    Sallet, Erika; Roux, Brice; Sauviac, Laurent; Jardinaud, Marie-Franc¸oise; Carrère, Sébastien; Faraut, Thomas; de Carvalho-Niebel, Fernanda; Gouzy, Jérôme; Gamas, Pascal; Capela, Delphine; Bruand, Claude; Schiex, Thomas

    2013-01-01

    The availability of next-generation sequences of transcripts from prokaryotic organisms offers the opportunity to design a new generation of automated genome annotation tools not yet available for prokaryotes. In this work, we designed EuGene-P, the first integrative prokaryotic gene finder tool which combines a variety of high-throughput data, including oriented RNA-Seq data, directly into the prediction process. This enables the automated prediction of coding sequences (CDSs), untranslated regions, transcription start sites (TSSs) and non-coding RNA (ncRNA, sense and antisense) genes. EuGene-P was used to comprehensively and accurately annotate the genome of the nitrogen-fixing bacterium Sinorhizobium meliloti strain 2011, leading to the prediction of 6308 CDSs as well as 1876 ncRNAs. Among them, 1280 appeared as antisense to a CDS, which supports recent findings that antisense transcription activity is widespread in bacteria. Moreover, 4077 TSSs upstream of protein-coding or non-coding genes were precisely mapped providing valuable data for the study of promoter regions. By looking for RpoE2-binding sites upstream of annotated TSSs, we were able to extend the S. meliloti RpoE2 regulon by ∼3-fold. Altogether, these observations demonstrate the power of EuGene-P to produce a reliable and high-resolution automatic annotation of prokaryotic genomes. PMID:23599422

  20. Next-generation annotation of prokaryotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011.

    PubMed

    Sallet, Erika; Roux, Brice; Sauviac, Laurent; Jardinaud, Marie-Francoise; Carrère, Sébastien; Faraut, Thomas; de Carvalho-Niebel, Fernanda; Gouzy, Jérôme; Gamas, Pascal; Capela, Delphine; Bruand, Claude; Schiex, Thomas

    2013-08-01

    The availability of next-generation sequences of transcripts from prokaryotic organisms offers the opportunity to design a new generation of automated genome annotation tools not yet available for prokaryotes. In this work, we designed EuGene-P, the first integrative prokaryotic gene finder tool which combines a variety of high-throughput data, including oriented RNA-Seq data, directly into the prediction process. This enables the automated prediction of coding sequences (CDSs), untranslated regions, transcription start sites (TSSs) and non-coding RNA (ncRNA, sense and antisense) genes. EuGene-P was used to comprehensively and accurately annotate the genome of the nitrogen-fixing bacterium Sinorhizobium meliloti strain 2011, leading to the prediction of 6308 CDSs as well as 1876 ncRNAs. Among them, 1280 appeared as antisense to a CDS, which supports recent findings that antisense transcription activity is widespread in bacteria. Moreover, 4077 TSSs upstream of protein-coding or non-coding genes were precisely mapped providing valuable data for the study of promoter regions. By looking for RpoE2-binding sites upstream of annotated TSSs, we were able to extend the S. meliloti RpoE2 regulon by ∼3-fold. Altogether, these observations demonstrate the power of EuGene-P to produce a reliable and high-resolution automatic annotation of prokaryotic genomes. PMID:23599422

  1. Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome

    PubMed Central

    2010-01-01

    Background Brucellosis is a major bacterial zoonosis affecting domestic livestock and wild mammals, as well as humans around the globe. While conducting proteomics studies to better understand Brucella abortus virulence, we consolidated the proteomic data collected and compared it to publically available genomic data. Results The proteomic data was compiled from several independent comparative studies of Brucella abortus that used either outer membrane blebs, cytosols, or whole bacteria grown in media, as well as intracellular bacteria recovered at different times following macrophage infection. We identified a total of 621 bacterial proteins that were differentially expressed in a condition-specific manner. For 305 of these proteins we provide the first experimental evidence of their expression. Using a custom-built protein sequence database, we uncovered 7 annotation errors. We provide experimental evidence of expression of 5 genes that were originally annotated as non-expressed pseudogenes, as well as start site annotation errors for 2 other genes. Conclusions An essential element for ensuring correct functional studies is the correspondence between reported genome sequences and subsequent proteomics studies. In this study, we have used proteomics evidence to confirm expression of multiple proteins previously considered to be putative, as well as correct annotation errors in the genome of Brucella abortus strain 2308. PMID:20462421

  2. Target Selection and Annotation for the Structural Genomics of the Amidohydrolase and Enolase Superfamilies

    SciTech Connect

    Pieper, U.; Chiang, R; Seffernick, J; Brown, S; Glasner, M; Kelly, L; Eswar, N; Sauder, M; Bonanno, J; et al,

    2009-01-01

    To study the substrate specificity of enzymes, we use the amidohydrolase and enolase superfamilies as model systems; members of these superfamilies share a common TIM barrel fold and catalyze a wide range of chemical reactions. Here, we describe a collaboration between the Enzyme Specificity Consortium (ENSPEC) and the New York SGX Research Center for Structural Genomics (NYSGXRC) that aims to maximize the structural coverage of the amidohydrolase and enolase superfamilies. Using sequence- and structure-based protein comparisons, we first selected 535 target proteins from a variety of genomes for high-throughput structure determination by X-ray crystallography; 63 of these targets were not previously annotated as superfamily members. To date, 20 unique amidohydrolase and 41 unique enolase structures have been determined, increasing the fraction of sequences in the two superfamilies that can be modeled based on at least 30% sequence identity from 45% to 73%. We present case studies of proteins related to uronate isomerase (an amidohydrolase superfamily member) and mandelate racemase (an enolase superfamily member), to illustrate how this structure-focused approach can be used to generate hypotheses about sequence-structure-function relationships.

  3. Integration and Querying of Genomic and Proteomic Semantic Annotations for Biomedical Knowledge Extraction.

    PubMed

    Masseroli, Marco; Canakoglu, Arif; Ceri, Stefano

    2016-01-01

    Understanding complex biological phenomena involves answering complex biomedical questions on multiple biomolecular information simultaneously, which are expressed through multiple genomic and proteomic semantic annotations scattered in many distributed and heterogeneous data sources; such heterogeneity and dispersion hamper the biologists' ability of asking global queries and performing global evaluations. To overcome this problem, we developed a software architecture to create and maintain a Genomic and Proteomic Knowledge Base (GPKB), which integrates several of the most relevant sources of such dispersed information (including Entrez Gene, UniProt, IntAct, Expasy Enzyme, GO, GOA, BioCyc, KEGG, Reactome, and OMIM). Our solution is general, as it uses a flexible, modular, and multilevel global data schema based on abstraction and generalization of integrated data features, and a set of automatic procedures for easing data integration and maintenance, also when the integrated data sources evolve in data content, structure, and number. These procedures also assure consistency, quality, and provenance tracking of all integrated data, and perform the semantic closure of the hierarchical relationships of the integrated biomedical ontologies. At http://www.bioinformatics.deib.polimi.it/GPKB/, a Web interface allows graphical easy composition of queries, although complex, on the knowledge base, supporting also semantic query expansion and comprehensive explorative search of the integrated data to better sustain biomedical knowledge extraction. PMID:27045824

  4. An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome

    PubMed Central

    Hild, M; Beckmann, B; Haas, SA; Koch, B; Solovyev, V; Busold, C; Fellenberg, K; Boutros, M; Vingron, M; Sauer, F; Hoheisel, JD; Paro, R

    2004-01-01

    Background While the genome sequences for a variety of organisms are now available, the precise number of the genes encoded is still a matter of debate. For the human genome several stringent annotation approaches have resulted in the same number of potential genes, but a careful comparison revealed only limited overlap. This indicates that only the combination of different computational prediction methods and experimental evaluation of such in silico data will provide more complete genome annotations. In order to get a more complete gene content of the Drosophila melanogaster genome, we based our new D. melanogaster whole-transcriptome microarray, the Heidelberg FlyArray, on the combination of the Berkeley Drosophila Genome Project (BDGP) annotation and a novel ab initio gene prediction of lower stringency using the Fgenesh software. Results Here we provide evidence for the transcription of approximately 2,600 additional genes predicted by Fgenesh. Validation of the developmental profiling data by RT-PCR and in situ hybridization indicates a lower limit of 2,000 novel annotations, thus substantially raising the number of genes that make a fly. Conclusions The successful design and application of this novel Drosophila microarray on the basis of our integrated in silico/wet biology approach confirms our expectation that in silico approaches alone will always tend to be incomplete. The identification of at least 2,000 novel genes highlights the importance of gathering experimental evidence to discover all genes within a genome. Moreover, as such an approach is independent of homology criteria, it will allow the discovery of novel genes unrelated to known protein families or those that have not been strictly conserved between species. PMID:14709175

  5. Leveraging Genomic Annotations and Pleiotropic Enrichment for Improved Replication Rates in Schizophrenia GWAS

    PubMed Central

    Wang, Yunpeng; Thompson, Wesley K.; Schork, Andrew J.; Holland, Dominic; Chen, Chi-Hua; Bettella, Francesco; Desikan, Rahul S.; Li, Wen; Witoelar, Aree; Zuber, Verena; Devor, Anna; Nöthen, Markus M.; Rietschel, Marcella; Chen, Qiang; Werge, Thomas; Cichon, Sven; Weinberger, Daniel R.; Djurovic, Srdjan; O’Donovan, Michael; Visscher, Peter M.; Andreassen, Ole A.; Dale, Anders M.

    2016-01-01

    Most of the genetic architecture of schizophrenia (SCZ) has not yet been identified. Here, we apply a novel statistical algorithm called Covariate-Modulated Mixture Modeling (CM3), which incorporates auxiliary information (heterozygosity, total linkage disequilibrium, genomic annotations, pleiotropy) for each single nucleotide polymorphism (SNP) to enable more accurate estimation of replication probabilities, conditional on the observed test statistic (“z-score”) of the SNP. We use a multiple logistic regression on z-scores to combine information from auxiliary information to derive a “relative enrichment score” for each SNP. For each stratum of these relative enrichment scores, we obtain nonparametric estimates of posterior expected test statistics and replication probabilities as a function of discovery z-scores, using a resampling-based approach that repeatedly and randomly partitions meta-analysis sub-studies into training and replication samples. We fit a scale mixture of two Gaussians model to each stratum, obtaining parameter estimates that minimize the sum of squared differences of the scale-mixture model with the stratified nonparametric estimates. We apply this approach to the recent genome-wide association study (GWAS) of SCZ (n = 82,315), obtaining a good fit between the model-based and observed effect sizes and replication probabilities. We observed that SNPs with low enrichment scores replicate with a lower probability than SNPs with high enrichment scores even when both they are genome-wide significant (p < 5x10-8). There were 693 and 219 independent loci with model-based replication rates ≥80% and ≥90%, respectively. Compared to analyses not incorporating relative enrichment scores, CM3 increased out-of-sample yield for SNPs that replicate at a given rate. This demonstrates that replication probabilities can be more accurately estimated using prior enrichment information with CM3. PMID:26808560

  6. Leveraging Genomic Annotations and Pleiotropic Enrichment for Improved Replication Rates in Schizophrenia GWAS.

    PubMed

    Wang, Yunpeng; Thompson, Wesley K; Schork, Andrew J; Holland, Dominic; Chen, Chi-Hua; Bettella, Francesco; Desikan, Rahul S; Li, Wen; Witoelar, Aree; Zuber, Verena; Devor, Anna; Nöthen, Markus M; Rietschel, Marcella; Chen, Qiang; Werge, Thomas; Cichon, Sven; Weinberger, Daniel R; Djurovic, Srdjan; O'Donovan, Michael; Visscher, Peter M; Andreassen, Ole A; Dale, Anders M

    2016-01-01

    Most of the genetic architecture of schizophrenia (SCZ) has not yet been identified. Here, we apply a novel statistical algorithm called Covariate-Modulated Mixture Modeling (CM3), which incorporates auxiliary information (heterozygosity, total linkage disequilibrium, genomic annotations, pleiotropy) for each single nucleotide polymorphism (SNP) to enable more accurate estimation of replication probabilities, conditional on the observed test statistic ("z-score") of the SNP. We use a multiple logistic regression on z-scores to combine information from auxiliary information to derive a "relative enrichment score" for each SNP. For each stratum of these relative enrichment scores, we obtain nonparametric estimates of posterior expected test statistics and replication probabilities as a function of discovery z-scores, using a resampling-based approach that repeatedly and randomly partitions meta-analysis sub-studies into training and replication samples. We fit a scale mixture of two Gaussians model to each stratum, obtaining parameter estimates that minimize the sum of squared differences of the scale-mixture model with the stratified nonparametric estimates. We apply this approach to the recent genome-wide association study (GWAS) of SCZ (n = 82,315), obtaining a good fit between the model-based and observed effect sizes and replication probabilities. We observed that SNPs with low enrichment scores replicate with a lower probability than SNPs with high enrichment scores even when both they are genome-wide significant (p < 5x10-8). There were 693 and 219 independent loci with model-based replication rates ≥80% and ≥90%, respectively. Compared to analyses not incorporating relative enrichment scores, CM3 increased out-of-sample yield for SNPs that replicate at a given rate. This demonstrates that replication probabilities can be more accurately estimated using prior enrichment information with CM3. PMID:26808560

  7. Dry and wet approaches for genome-wide functional annotation of conventional and unconventional transcriptional activators.

    PubMed

    Levati, Elisabetta; Sartini, Sara; Ottonello, Simone; Montanini, Barbara

    2016-01-01

    Transcription factors (TFs) are master gene products that regulate gene expression in response to a variety of stimuli. They interact with DNA in a sequence-specific manner using a variety of DNA-binding domain (DBD) modules. This allows to properly position their second domain, called "effector domain", to directly or indirectly recruit positively or negatively acting co-regulators including chromatin modifiers, thus modulating preinitiation complex formation as well as transcription elongation. At variance with the DBDs, which are comprised of well-defined and easily recognizable DNA binding motifs, effector domains are usually much less conserved and thus considerably more difficult to predict. Also not so easy to identify are the DNA-binding sites of TFs, especially on a genome-wide basis and in the case of overlapping binding regions. Another emerging issue, with many potential regulatory implications, is that of so-called "moonlighting" transcription factors, i.e., proteins with an annotated function unrelated to transcription and lacking any recognizable DBD or effector domain, that play a role in gene regulation as their second job. Starting from bioinformatic and experimental high-throughput tools for an unbiased, genome-wide identification and functional characterization of TFs (especially transcriptional activators), we describe both established (and usually well affordable) as well as newly developed platforms for DNA-binding site identification. Selected combinations of these search tools, some of which rely on next-generation sequencing approaches, allow delineating the entire repertoire of TFs and unconventional regulators encoded by the any sequenced genome. PMID:27453771

  8. Gene prediction and annotation in Penstemon (Plantaginaceae): A workflow for marker development from extremely low-coverage genome sequencing1

    PubMed Central

    Blischak, Paul D.; Wenzel, Aaron J.; Wolfe, Andrea D.

    2014-01-01

    • Premise of the study: Penstemon (Plantaginaceae) is a large and diverse genus endemic to North America. However, determining the phylogenetic relationships among its 280 species has been difficult due to its recent evolutionary radiation. The development of a large, multilocus data set can help to resolve this challenge. • Methods: Using both previously sequenced genomic libraries and our own low-coverage whole-genome shotgun sequencing libraries, we used the MAKER2 Annotation Pipeline to identify gene regions for the development of sequencing loci from six extremely low-coverage Penstemon genomes (∼0.005×–0.007×). We also compared this approach to BLAST searches, and conducted analyses to characterize sequence divergence across the species sequenced. • Results: Annotations and gene predictions were successfully added to more than 10,000 contigs for potential use in downstream primer design. Primers were then designed for chloroplast, mitochondrial, and nuclear loci from these annotated sequences. MAKER2 identified longer gene regions in all six Penstemon genomes when compared with BLASTN and BLASTX searches. The average level of sequence divergence among the six species was 7.14%. • Discussion: Combining bioinformatics tools into a workflow that produces annotations can be useful for creating potential phylogenetic markers from thousands of sequences even when genome coverage is extremely low and reference data are only available from distant relatives. Furthermore, the output from MAKER2 contains information about important gene features, such as exon boundaries, and can be easily integrated with visualization tools to facilitate the process of marker development. PMID:25506519

  9. Discovery of germline-related genes in Cephalochordate amphioxus: A genome wide survey using genome annotation and transcriptome data.

    PubMed

    Yue, Jia-Xing; Li, Kun-Lung; Yu, Jr-Kai

    2015-12-01

    The generation of germline cells is a critical process in the reproduction of multicellular organisms. Studies in animal models have identified a common repertoire of genes that play essential roles in primordial germ cell (PGC) formation. However, comparative studies also indicate that the timing and regulation of this core genetic program vary considerably in different animals, raising the intriguing questions regarding the evolution of PGC developmental mechanisms in metazoans. Cephalochordates (commonly called amphioxus or lancelets) represent one of the invertebrate chordate groups and can provide important information about the evolution of developmental mechanisms in the chordate lineage. In this study, we used genome and transcriptome data to identify germline-related genes in two distantly related cephalochordate species, Branchiostoma floridae and Asymmetron lucayanum. Branchiostoma and Asymmetron diverged more than 120 MYA, and the most conspicuous difference between them is their gonadal morphology. We used important germline developmental genes in several model animals to search the amphioxus genome and transcriptome dataset for conserved homologs. We also annotated the assembled transcriptome data using Gene Ontology (GO) terms to facilitate the discovery of putative genes associated with germ cell development and reproductive functions in amphioxus. We further confirmed the expression of 14 genes in developing oocytes or mature eggs using whole mount in situ hybridization, suggesting their potential functions in amphioxus germ cell development. The results of this global survey provide a useful resource for testing potential functions of candidate germline-related genes in cephalochordates and for investigating differences in gonad developmental mechanisms between Branchiostoma and Asymmetron species. PMID:25847029

  10. Comparative annotation of functional regions in the human genome using epigenomic data

    PubMed Central

    Won, Kyoung-Jae; Zhang, Xian; Wang, Tao; Ding, Bo; Raha, Debasish; Snyder, Michael; Ren, Bing; Wang, Wei

    2013-01-01

    Epigenetic regulation is dynamic and cell-type dependent. The recently available epigenomic data in multiple cell types provide an unprecedented opportunity for a comparative study of epigenetic landscape. We developed a machine-learning method called ChroModule to annotate the epigenetic states in eight ENCyclopedia Of DNA Elements cell types. The trained model successfully captured the characteristic histone-modification patterns associated with regulatory elements, such as promoters and enhancers, and showed superior performance on identifying enhancers compared with the state-of-art methods. In addition, given the fixed number of epigenetic states in the model, ChroModule allows straightforward illustration of epigenetic variability in multiple cell types. Using this feature, we found that invariable and variable epigenetic states across cell types correspond to housekeeping functions and stimulus response, respectively. Especially, we observed that enhancers, but not the other regulatory elements, dictate cell specificity, as similar cell types share common enhancers, and cell-type–specific enhancers are often bound by transcription factors playing critical roles in that cell type. More interestingly, we found some genomic regions are dormant in cell type but primed to become active in other cell types. These observations highlight the usefulness of ChroModule in comparative analysis and interpretation of multiple epigenomes. PMID:23482391

  11. Comparative annotation of functional regions in the human genome using epigenomic data.

    PubMed

    Won, Kyoung-Jae; Zhang, Xian; Wang, Tao; Ding, Bo; Raha, Debasish; Snyder, Michael; Ren, Bing; Wang, Wei

    2013-04-01

    Epigenetic regulation is dynamic and cell-type dependent. The recently available epigenomic data in multiple cell types provide an unprecedented opportunity for a comparative study of epigenetic landscape. We developed a machine-learning method called ChroModule to annotate the epigenetic states in eight ENCyclopedia Of DNA Elements cell types. The trained model successfully captured the characteristic histone-modification patterns associated with regulatory elements, such as promoters and enhancers, and showed superior performance on identifying enhancers compared with the state-of-art methods. In addition, given the fixed number of epigenetic states in the model, ChroModule allows straightforward illustration of epigenetic variability in multiple cell types. Using this feature, we found that invariable and variable epigenetic states across cell types correspond to housekeeping functions and stimulus response, respectively. Especially, we observed that enhancers, but not the other regulatory elements, dictate cell specificity, as similar cell types share common enhancers, and cell-type-specific enhancers are often bound by transcription factors playing critical roles in that cell type. More interestingly, we found some genomic regions are dormant in cell type but primed to become active in other cell types. These observations highlight the usefulness of ChroModule in comparative analysis and interpretation of multiple epigenomes. PMID:23482391

  12. The genome sequence of Leishmania (Leishmania) amazonensis: functional annotation and extended analysis of gene models.

    PubMed

    Real, Fernando; Vidal, Ramon Oliveira; Carazzolle, Marcelo Falsarella; Mondego, Jorge Maurício Costa; Costa, Gustavo Gilson Lacerda; Herai, Roberto Hirochi; Würtele, Martin; de Carvalho, Lucas Miguel; Carmona e Ferreira, Renata; Mortara, Renato Arruda; Barbiéri, Clara Lucia; Mieczkowski, Piotr; da Silveira, José Franco; Briones, Marcelo Ribeiro da Silva; Pereira, Gonçalo Amarante Guimarães; Bahia, Diana

    2013-12-01

    We present the sequencing and annotation of the Leishmania (Leishmania) amazonensis genome, an etiological agent of human cutaneous leishmaniasis in the Amazon region of Brazil. L. (L.) amazonensis shares features with Leishmania (L.) mexicana but also exhibits unique characteristics regarding geographical distribution and clinical manifestations of cutaneous lesions (e.g. borderline disseminated cutaneous leishmaniasis). Predicted genes were scored for orthologous gene families and conserved domains in comparison with other human pathogenic Leishmania spp. Carboxypeptidase, aminotransferase, and 3'-nucleotidase genes and ATPase, thioredoxin, and chaperone-related domains were represented more abundantly in L. (L.) amazonensis and L. (L.) mexicana species. Phylogenetic analysis revealed that these two species share groups of amastin surface proteins unique to the genus that could be related to specific features of disease outcomes and host cell interactions. Additionally, we describe a hypothetical hybrid interactome of potentially secreted L. (L.) amazonensis proteins and host proteins under the assumption that parasite factors mimic their mammalian counterparts. The model predicts an interaction between an L. (L.) amazonensis heat-shock protein and mammalian Toll-like receptor 9, which is implicated in important immune responses such as cytokine and nitric oxide production. The analysis presented here represents valuable information for future studies of leishmaniasis pathogenicity and treatment. PMID:23857904

  13. Narrowing and genomic annotation of the commonly deleted region of the 5q- syndrome

    SciTech Connect

    Boultwood, Jacqueline; Fidler, Carrie; Strickson, Amanda J.; Watkins, Fiona; Gama, Susana; Kearney, Lyndal; Tosi, Sabrina; Kasprzyk, Arek; Cheng, Jan-Fang; Jaju, Rina J.; Wainscoat, James S.

    2002-01-15

    The 5q syndrome is the most distinct of the myelodysplastic syndromes, and the molecular basis for this disorder remains unknown. We describe the narrowing of the common deleted region (CDR) of the 5q syndrome to the approximately 1.5-megabases interval at 5q32 flanked by D5S413 and the GLRA1 gene. The Ensemblgene prediction program has been used for the complete genomic annotation of the CDR. The CDR is gene rich and contains 24 known genes and 16 novel (predicted) genes. Of 40 genes in the CDR, 33 are expressed in CD34 cells and, therefore, represent candidate genes since they are expressed within the hematopoietic stem/progenitor cell compartment. A number of the genes assigned to the CDR represent good candidates for the 5q syndrome, including MEGF1, G3BP, and several of the novel gene predictions. These data now afford a comprehensive mutational/expression analysis of all candidate genes assigned to the CDR.

  14. Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models

    DOE PAGESBeta

    Benedict, Matthew N.; Mundy, Michael B.; Henry, Christopher S.; Chia, Nicholas; Price, Nathan D.; Maranas, Costas D.

    2014-10-16

    Genome-scale metabolic models provide a powerful means to harness information from genomes to deepen biological insights. With exponentially increasing sequencing capacity, there is an enormous need for automated reconstruction techniques that can provide more accurate models in a short time frame. Current methods for automated metabolic network reconstruction rely on gene and reaction annotations to build draft metabolic networks and algorithms to fill gaps in these networks. However, automated reconstruction is hampered by database inconsistencies, incorrect annotations, and gap filling largely without considering genomic information. Here we develop an approach for applying genomic information to predict alternative functions for genesmore » and estimate their likelihoods from sequence homology. We show that computed likelihood values were significantly higher for annotations found in manually curated metabolic networks than those that were not. We then apply these alternative functional predictions to estimate reaction likelihoods, which are used in a new gap filling approach called likelihood-based gap filling to predict more genomically consistent solutions. To validate the likelihood-based gap filling approach, we applied it to models where essential pathways were removed, finding that likelihood-based gap filling identified more biologically relevant solutions than parsimony-based gap filling approaches. We also demonstrate that models gap filled using likelihood-based gap filling provide greater coverage and genomic consistency with metabolic gene functions compared to parsimony-based approaches. Interestingly, despite these findings, we found that likelihoods did not significantly affect consistency of gap filled models with Biolog and knockout lethality data. This indicates that the phenotype data alone cannot necessarily be used to discriminate between alternative solutions for gap filling and therefore, that the use of other information is necessary

  15. Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models

    SciTech Connect

    Benedict, Matthew N.; Mundy, Michael B.; Henry, Christopher S.; Chia, Nicholas; Price, Nathan D.; Maranas, Costas D.

    2014-10-16

    Genome-scale metabolic models provide a powerful means to harness information from genomes to deepen biological insights. With exponentially increasing sequencing capacity, there is an enormous need for automated reconstruction techniques that can provide more accurate models in a short time frame. Current methods for automated metabolic network reconstruction rely on gene and reaction annotations to build draft metabolic networks and algorithms to fill gaps in these networks. However, automated reconstruction is hampered by database inconsistencies, incorrect annotations, and gap filling largely without considering genomic information. Here we develop an approach for applying genomic information to predict alternative functions for genes and estimate their likelihoods from sequence homology. We show that computed likelihood values were significantly higher for annotations found in manually curated metabolic networks than those that were not. We then apply these alternative functional predictions to estimate reaction likelihoods, which are used in a new gap filling approach called likelihood-based gap filling to predict more genomically consistent solutions. To validate the likelihood-based gap filling approach, we applied it to models where essential pathways were removed, finding that likelihood-based gap filling identified more biologically relevant solutions than parsimony-based gap filling approaches. We also demonstrate that models gap filled using likelihood-based gap filling provide greater coverage and genomic consistency with metabolic gene functions compared to parsimony-based approaches. Interestingly, despite these findings, we found that likelihoods did not significantly affect consistency of gap filled models with Biolog and knockout lethality data. This indicates that the phenotype data alone cannot necessarily be used to discriminate between alternative solutions for gap filling and therefore, that the use of other information is necessary to

  16. Draft genome sequence and annotation of Lactobacillus acetotolerans BM-LA14527, a beer-spoilage bacteria.

    PubMed

    Liu, Junyan; Li, Lin; Peters, Brian M; Li, Bing; Deng, Yang; Xu, Zhenbo; Shirtliff, Mark E

    2016-09-01

    Lactobacillus acetotolerans is a hard-to-culture beer-spoilage bacterium capable of entering into the viable putative nonculturable (VPNC) state. As part of an initial strategy to investigate the phenotypic behavior of L. acetotolerans, draft genome sequencing was performed. Results demonstrated a total of 1824 predicted annotated genes, with several potential VPNC- and beer-spoilage-associated genes identified. Importantly, this is the first genome sequence of L. acetotolerans as beer-spoilage bacteria and it may aid in further analysis of L. acetotolerans and other beer-spoilage bacteria, with direct implications for food safety control in the beer brewing industry. PMID:27559043

  17. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

    PubMed Central

    2012-01-01

    Background The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need. Results We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR) are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities. Conclusions CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas. PMID:23256920

  18. The Otter Annotation System

    PubMed Central

    Searle, Stephen M.J.; Gilbert, James; Iyer, Vivek; Clamp, Michele

    2004-01-01

    With the completion of the human genome sequence and genome sequence available for other vertebrate genomes, the task of manual annotation at the large genome scale has become a priority. Possibly even more important, is the requirement to curate and improve this annotation in the light of future data. For this to be possible, there is a need for tools to access and manage the annotation. Ensembl provides an excellent means for storing gene structures, genome features, and sequence, but it does not support the extra textual data necessary for manual annotation. We have extended Ensembl to create the Otter manual annotation system. This comprises a relational database schema for storing the manual annotation data, an application-programming interface (API) to access it, an extensible markup language (XML) format to allow transfer of the data, and a server to allow multiuser/multimachine access to the data. We have also written a data-adaptor plugin for the Apollo Browser/Editor to enable it to utilize an Otter server. The otter database is currently used by the Vertebrate Genome Annotation (VEGA) site (http://vega.sanger.ac.uk), which provides access to manually curated human chromosomes. Support is also being developed for using the AceDB annotation editor, FMap, via a perl wrapper called Lace. The Human and Vertebrate Annotation (HAVANA) group annotators at the Sanger center are using this to annotate human chromosomes 1 and 20. PMID:15123593

  19. Computational prediction of over-annotated protein-coding genes in the genome of Agrobacterium tumefaciens strain C58

    NASA Astrophysics Data System (ADS)

    Yu, Jia-Feng; Sui, Tian-Xiang; Wang, Hong-Mei; Wang, Chun-Ling; Jing, Li; Wang, Ji-Hua

    2015-12-01

    Agrobacterium tumefaciens strain C58 is a type of pathogen that can cause tumors in some dicotyledonous plants. Ever since the genome of A. tumefaciens strain C58 was sequenced, the quality of annotation of its protein-coding genes has been queried continually, because the annotation varies greatly among different databases. In this paper, the questionable hypothetical genes were re-predicted by integrating the TN curve and Z curve methods. As a result, 30 genes originally annotated as “hypothetical” were discriminated as being non-coding sequences. By testing the re-prediction program 10 times on data sets composed of the function-known genes, the mean accuracy of 99.99% and mean Matthews correlation coefficient value of 0.9999 were obtained. Further sequence analysis and COG analysis showed that the re-annotation results were very reliable. This work can provide an efficient tool and data resources for future studies of A. tumefaciens strain C58. Project supported by the National Natural Science Foundation of China (Grant Nos. 61302186 and 61271378) and the Funding from the State Key Laboratory of Bioelectronics of Southeast University.

  20. ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera.

    PubMed

    Lewis, James J; van der Burg, Karin R L; Mazo-Vargas, Anyi; Reed, Robert D

    2016-09-13

    Uncovering phylogenetic patterns of cis-regulatory evolution remains a fundamental goal for evolutionary and developmental biology. Here, we characterize the evolution of regulatory loci in butterflies and moths using chromatin immunoprecipitation sequencing (ChIP-seq) annotation of regulatory elements across three stages of head development. In the process we provide a high-quality, functionally annotated genome assembly for the butterfly, Heliconius erato. Comparing cis-regulatory element conservation across six lepidopteran genomes, we find that regulatory sequences evolve at a pace similar to that of protein-coding regions. We also observe that elements active at multiple developmental stages are markedly more conserved than elements with stage-specific activity. Surprisingly, we also find that stage-specific proximal and distal regulatory elements evolve at nearly identical rates. Our study provides a benchmark for genome-wide patterns of regulatory element evolution in insects, and it shows that developmental timing of activity strongly predicts patterns of regulatory sequence evolution. PMID:27626657

  1. The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database

    PubMed Central

    Engel, Stacia R.; Cherry, J. Michael

    2013-01-01

    The first completed eukaryotic genome sequence was that of the yeast Saccharomyces cerevisiae, and the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the original model organism database. SGD remains the authoritative community resource for the S. cerevisiae reference genome sequence and its annotation, and continues to provide comprehensive biological information correlated with S. cerevisiae genes and their products. A diverse set of yeast strains have been sequenced to explore commercial and laboratory applications, and a brief history of those strains is provided. The publication of these new genomes has motivated the creation of new tools, and SGD will annotate and provide comparative analyses of these sequences, correlating changes with variations in strain phenotypes and protein function. We are entering a new era at SGD, as we incorporate these new sequences and make them accessible to the scientific community, all in an effort to continue in our mission of educating researchers and facilitating discovery. Database URL: http://www.yeastgenome.org/ PMID:23487186

  2. An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

    PubMed Central

    2010-01-01

    Background A comprehensive transcriptome survey, or gene atlas, provides information essential for a complete understanding of the genomic biology of an organism. We present an atlas of RNA abundance for 92 adult, juvenile and fetal cattle tissues and three cattle cell lines. Results The Bovine Gene Atlas was generated from 7.2 million unique digital gene expression tag sequences (300.2 million total raw tag sequences), from which 1.59 million unique tag sequences were identified that mapped to the draft bovine genome accounting for 85% of the total raw tag abundance. Filtering these tags yielded 87,764 unique tag sequences that unambiguously mapped to 16,517 annotated protein-coding loci in the draft genome accounting for 45% of the total raw tag abundance. Clustering of tissues based on tag abundance profiles generally confirmed ontology classification based on anatomy. There were 5,429 constitutively expressed loci and 3,445 constitutively expressed unique tag sequences mapping outside annotated gene boundaries that represent a resource for enhancing current gene models. Physical measures such as inferred transcript length or antisense tag abundance identified tissues with atypical transcriptional tag profiles. We report for the first time the tissue-specific variation in the proportion of mitochondrial transcriptional tag abundance. Conclusions The Bovine Gene Atlas is the deepest and broadest transcriptome survey of any livestock genome to date. Commonalities and variation in sense and antisense transcript tag profiles identified in different tissues facilitate the examination of the relationship between gene expression, tissue, and gene function. PMID:20961407

  3. Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

    PubMed

    Elnitski, Laura; Giardine, Belinda; Shah, Prachi; Zhang, Yi; Riemer, Cathy; Weirauch, Matthew; Burhans, Richard; Miller, Webb; Hardison, Ross C

    2005-01-01

    We describe improvements to two databases that give access to information on genomic sequence similarities, functional elements in DNA and experimental results that demonstrate those functions. GALA, the database of Genome ALignments and Annotations, is now a set of interlinked relational databases for five vertebrate species, human, chimpanzee, mouse, rat and chicken. For each species, GALA records pairwise and multiple sequence alignments, scores derived from those alignments that reflect the likelihood of being under purifying selection or being a regulatory element, and extensive annotations such as genes, gene expression patterns and transcription factor binding sites. The user interface supports simple and complex queries, including operations such as subtraction and intersections as well as clustering and finding elements in proximity to features. dbERGE II, the database of Experimental Results on Gene Expression, contains experimental data from a variety of functional assays. Both databases are now run on the DB2 database management system. Improved hardware and tuning has reduced response times and increased querying capacity, while simplified query interfaces will help direct new users through the querying process. Links are available at http://www.bx.psu.edu/. PMID:15608239

  4. SNPMeta: SNP annotation and SNP metadata collection without a reference genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The increase in availability of resequencing data is greatly accelerating SNP discovery and has facilitated the development of SNP genotyping assays. This, in turn, is increasing interest in annotation of individual SNPs. Currently, these data are only available through curation, or comparison to a ...

  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.

    PubMed

    Gaudet, Pascale; Livstone, Michael S; Lewis, Suzanna E; Thomas, Paul D

    2011-09-01

    The goal of the Gene Ontology (GO) project is to provide a uniform way to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data. Protein annotations are either based on experiments or predicted from protein sequences. Since most sequences have not been experimentally characterized, most available annotations need to be based on predictions. To make as accurate inferences as possible, the GO Consortium's Reference Genome Project is using an explicit evolutionary framework to infer annotations of proteins from a broad set of genomes from experimental annotations in a semi-automated manner. Most components in the pipeline, such as selection of sequences, building multiple sequence alignments and phylogenetic trees, retrieving experimental annotations and depositing inferred annotations, are fully automated. However, the most crucial step in our pipeline relies on software-assisted curation by an expert biologist. This curation tool, Phylogenetic Annotation and INference Tool (PAINT) helps curators to infer annotations among members of a protein family. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions. In this article, we describe how we use PAINT to infer protein function in a phylogenetic context with emphasis on its strengths, limitations and guidelines. We also discuss specific examples showing how PAINT annotations compare with those generated by other highly used homology-based methods. PMID:21873635

  6. Comparative Life Cycle Transcriptomics Revises Leishmania mexicana Genome Annotation and Links a Chromosome Duplication with Parasitism of Vertebrates

    PubMed Central

    Fiebig, Michael; Kelly, Steven; Gluenz, Eva

    2015-01-01

    Leishmania spp. are protozoan parasites that have two principal life cycle stages: the motile promastigote forms that live in the alimentary tract of the sandfly and the amastigote forms, which are adapted to survive and replicate in the harsh conditions of the phagolysosome of mammalian macrophages. Here, we used Illumina sequencing of poly-A selected RNA to characterise and compare the transcriptomes of L. mexicana promastigotes, axenic amastigotes and intracellular amastigotes. These data allowed the production of the first transcriptome evidence-based annotation of gene models for this species, including genome-wide mapping of trans-splice sites and poly-A addition sites. The revised genome annotation encompassed 9,169 protein-coding genes including 936 novel genes as well as modifications to previously existing gene models. Comparative analysis of gene expression across promastigote and amastigote forms revealed that 3,832 genes are differentially expressed between promastigotes and intracellular amastigotes. A large proportion of genes that were downregulated during differentiation to amastigotes were associated with the function of the motile flagellum. In contrast, those genes that were upregulated included cell surface proteins, transporters, peptidases and many uncharacterized genes, including 293 of the 936 novel genes. Genome-wide distribution analysis of the differentially expressed genes revealed that the tetraploid chromosome 30 is highly enriched for genes that were upregulated in amastigotes, providing the first evidence of a link between this whole chromosome duplication event and adaptation to the vertebrate host in this group. Peptide evidence for 42 proteins encoded by novel transcripts supports the idea of an as yet uncharacterised set of small proteins in Leishmania spp. with possible implications for host-pathogen interactions. PMID:26452044

  7. Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes1[OPEN

    PubMed Central

    Law, MeiYee; Childs, Kevin L.; Campbell, Michael S.; Stein, Joshua C.; Olson, Andrew J.; Holt, Carson; Panchy, Nicholas; Lei, Jikai; Jiao, Dian; Andorf, Carson M.; Lawrence, Carolyn J.; Ware, Doreen; Shiu, Shin-Han; Sun, Yanni; Jiang, Ning; Yandell, Mark

    2015-01-01

    The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-P to update and revise the maize (Zea mays) B73 RefGen_v3 annotation build (5b+) in less than 3 h using the iPlant Cyberinfrastructure. MAKER-P identified and annotated 4,466 additional, well-supported protein-coding genes not present in the 5b+ annotation build, added additional untranslated regions to 1,393 5b+ gene models, identified 2,647 5b+ gene models that lack any supporting evidence (despite the use of large and diverse evidence data sets), identified 104,215 pseudogene fragments, and created an additional 2,522 noncoding gene annotations. We also describe a method for de novo training of MAKER-P for the annotation of newly sequenced grass genomes. Collectively, these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P for rapid annotation, management, and quality control of grasses and other difficult-to-annotate plant genomes. PMID:25384563

  8. Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-...

  9. The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database.

    PubMed

    Hayman, G Thomas; Laulederkind, Stanley J F; Smith, Jennifer R; Wang, Shur-Jen; Petri, Victoria; Nigam, Rajni; Tutaj, Marek; De Pons, Jeff; Dwinell, Melinda R; Shimoyama, Mary

    2016-01-01

    The Rat Genome Database (RGD;http://rgd.mcw.edu/) provides critical datasets and software tools to a diverse community of rat and non-rat researchers worldwide. To meet the needs of the many users whose research is disease oriented, RGD has created a series of Disease Portals and has prioritized its curation efforts on the datasets important to understanding the mechanisms of various diseases. Gene-disease relationships for three species, rat, human and mouse, are annotated to capture biomarkers, genetic associations, molecular mechanisms and therapeutic targets. To generate gene-disease annotations more effectively and in greater detail, RGD initially adopted the MEDIC disease vocabulary from the Comparative Toxicogenomics Database and adapted it for use by expanding this framework with the addition of over 1000 terms to create the RGD Disease Ontology (RDO). The RDO provides the foundation for, at present, 10 comprehensive disease area-related dataset and analysis platforms at RGD, the Disease Portals. Two major disease areas are the focus of data acquisition and curation efforts each year, leading to the release of the related Disease Portals. Collaborative efforts to realize a more robust disease ontology are underway. Database URL:http://rgd.mcw.edu. PMID:27009807

  10. Rapid Annotation of Anonymous Sequences from Genome Projects Using Semantic Similarities and a Weighting Scheme in Gene Ontology

    PubMed Central

    Fontana, Paolo; Cestaro, Alessandro; Velasco, Riccardo; Formentin, Elide; Toppo, Stefano

    2009-01-01

    Background Large-scale sequencing projects have now become routine lab practice and this has led to the development of a new generation of tools involving function prediction methods, bringing the latter back to the fore. The advent of Gene Ontology, with its structured vocabulary and paradigm, has provided computational biologists with an appropriate means for this task. Methodology We present here a novel method called ARGOT (Annotation Retrieval of Gene Ontology Terms) that is able to process quickly thousands of sequences for functional inference. The tool exploits for the first time an integrated approach which combines clustering of GO terms, based on their semantic similarities, with a weighting scheme which assesses retrieved hits sharing a certain number of biological features with the sequence to be annotated. These hits may be obtained by different methods and in this work we have based ARGOT processing on BLAST results. Conclusions The extensive benchmark involved 10,000 protein sequences, the complete S. cerevisiae genome and a small subset of proteins for purposes of comparison with other available tools. The algorithm was proven to outperform existing methods and to be suitable for function prediction of single proteins due to its high degree of sensitivity, specificity and coverage. PMID:19247487

  11. The Disease Portals, disease–gene annotation and the RGD disease ontology at the Rat Genome Database

    PubMed Central

    Hayman, G. Thomas; Laulederkind, Stanley J. F.; Smith, Jennifer R.; Wang, Shur-Jen; Petri, Victoria; Nigam, Rajni; Tutaj, Marek; De Pons, Jeff; Dwinell, Melinda R.; Shimoyama, Mary

    2016-01-01

    The Rat Genome Database (RGD; http://rgd.mcw.edu/) provides critical datasets and software tools to a diverse community of rat and non-rat researchers worldwide. To meet the needs of the many users whose research is disease oriented, RGD has created a series of Disease Portals and has prioritized its curation efforts on the datasets important to understanding the mechanisms of various diseases. Gene-disease relationships for three species, rat, human and mouse, are annotated to capture biomarkers, genetic associations, molecular mechanisms and therapeutic targets. To generate gene–disease annotations more effectively and in greater detail, RGD initially adopted the MEDIC disease vocabulary from the Comparative Toxicogenomics Database and adapted it for use by expanding this framework with the addition of over 1000 terms to create the RGD Disease Ontology (RDO). The RDO provides the foundation for, at present, 10 comprehensive disease area-related dataset and analysis platforms at RGD, the Disease Portals. Two major disease areas are the focus of data acquisition and curation efforts each year, leading to the release of the related Disease Portals. Collaborative efforts to realize a more robust disease ontology are underway. Database URL: http://rgd.mcw.edu PMID:27009807

  12. The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes.

    PubMed

    Braconi Quintaje, Silvia; Orchard, Sandra

    2008-08-01

    Biomolecule phosphorylation by protein kinases is a fundamental cell signaling process in all living cells. Following the comprehensive cataloguing of the protein kinase complement of the human genome (Manning, G., Whyte, D. B., Martinez, R., Hunter, T., and Sudarsanam, S. (2002) The protein kinase complement of the human genome. Science 298, 1912-1934), this review will detail the state-of-the-art human and mouse kinase proteomes as provided in the UniProtKB/Swiss-Prot protein knowledgebase. The sequences of the 480 classical and up to 24 atypical protein kinases now believed to exist in the human genome and 484 classical and up to 24 atypical kinases within the mouse genome have been reviewed and, where necessary, revised. Extensive annotation has been added to each entry. In an era when a wealth of new databases is emerging on the Internet, UniProtKB/Swiss-Prot makes available to the scientific community the most up-to-date and in-depth annotation of these proteins with access to additional external resources linked from within each entry. Incorrect sequence annotations resulting from errors and artifacts have been eliminated. Each entry will be constantly reviewed and updated as new information becomes available with the orthologous enzymes in related species being annotated in a parallel effort and complete kinomes being completed as sequences become available. This ensures that the mammalian kinomes available from UniProtKB/Swiss-Prot are of a consistently high standard with each separate entry acting both as a valuable information resource and a central portal to a wealth of further detail via extensive cross-referencing. PMID:18436524

  13. Carbohydrate catabolic flexibility in the mammalian intestinal commensal Lactobacillus ruminis revealed by fermentation studies aligned to genome annotations

    PubMed Central

    2011-01-01

    Background Lactobacillus ruminis is a poorly characterized member of the Lactobacillus salivarius clade that is part of the intestinal microbiota of pigs, humans and other mammals. Its variable abundance in human and animals may be linked to historical changes over time and geographical differences in dietary intake of complex carbohydrates. Results In this study, we investigated the ability of nine L. ruminis strains of human and bovine origin to utilize fifty carbohydrates including simple sugars, oligosaccharides, and prebiotic polysaccharides. The growth patterns were compared with metabolic pathways predicted by annotation of a high quality draft genome sequence of ATCC 25644 (human isolate) and the complete genome of ATCC 27782 (bovine isolate). All of the strains tested utilized prebiotics including fructooligosaccharides (FOS), soybean-oligosaccharides (SOS) and 1,3:1,4-β-D-gluco-oligosaccharides to varying degrees. Six strains isolated from humans utilized FOS-enriched inulin, as well as FOS. In contrast, three strains isolated from cows grew poorly in FOS-supplemented medium. In general, carbohydrate utilisation patterns were strain-dependent and also varied depending on the degree of polymerisation or complexity of structure. Six putative operons were identified in the genome of the human isolate ATCC 25644 for the transport and utilisation of the prebiotics FOS, galacto-oligosaccharides (GOS), SOS, and 1,3:1,4-β-D-Gluco-oligosaccharides. One of these comprised a novel FOS utilisation operon with predicted capacity to degrade chicory-derived FOS. However, only three of these operons were identified in the ATCC 27782 genome that might account for the utilisation of only SOS and 1,3:1,4-β-D-Gluco-oligosaccharides. Conclusions This study has provided definitive genome-based evidence to support the fermentation patterns of nine strains of Lactobacillus ruminis, and has linked it to gene distribution patterns in strains from different sources. Furthermore

  14. VibrioBase: a model for next-generation genome and annotation database development.

    PubMed

    Choo, Siew Woh; Heydari, Hamed; Tan, Tze King; Siow, Cheuk Chuen; Beh, Ching Yew; Wee, Wei Yee; Mutha, Naresh V R; Wong, Guat Jah; Ang, Mia Yang; Yazdi, Amir Hessam

    2014-01-01

    To facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence database with the addition of unique analysis tools which could be valuable for the Vibrio research community. VibrioBase currently houses a total of 252 Vibrio genomes developed in a user-friendly manner and useful to enable the analysis of these genomic data, particularly in the field of comparative genomics. Besides general data browsing features, VibrioBase offers analysis tools such as BLAST interfaces and JBrowse genome browser. Other important features of this platform include our newly developed in-house tools, the pairwise genome comparison (PGC) tool, and pathogenomics profiling tool (PathoProT). The PGC tool is useful in the identification and comparative analysis of two genomes, whereas PathoProT is designed for comparative pathogenomics analysis of Vibrio strains. Both of these tools will enable researchers with little experience in bioinformatics to get meaningful information from Vibrio genomes with ease. We have tested the validity and suitability of these tools and features for use in the next-generation database development. PMID:25243218

  15. An Innovative Plant Genomics and Gene Annotation Program for High School, Community College, and University Faculty

    ERIC Educational Resources Information Center

    Hacisalihoglu, Gokhan; Hilgert, Uwe; Nash, E. Bruce; Micklos, David A.

    2008-01-01

    Today's biology educators face the challenge of training their students in modern molecular biology techniques including genomics and bioinformatics. The Dolan DNA Learning Center (DNALC) of Cold Spring Harbor Laboratory has developed and disseminated a bench- and computer-based plant genomics curriculum for biology faculty. In 2007, a five-day…

  16. VibrioBase: A Model for Next-Generation Genome and Annotation Database Development

    PubMed Central

    Choo, Siew Woh; Tan, Tze King; Mutha, Naresh V. R.; Wong, Guat Jah

    2014-01-01

    To facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence database with the addition of unique analysis tools which could be valuable for the Vibrio research community. VibrioBase currently houses a total of 252 Vibrio genomes developed in a user-friendly manner and useful to enable the analysis of these genomic data, particularly in the field of comparative genomics. Besides general data browsing features, VibrioBase offers analysis tools such as BLAST interfaces and JBrowse genome browser. Other important features of this platform include our newly developed in-house tools, the pairwise genome comparison (PGC) tool, and pathogenomics profiling tool (PathoProT). The PGC tool is useful in the identification and comparative analysis of two genomes, whereas PathoProT is designed for comparative pathogenomics analysis of Vibrio strains. Both of these tools will enable researchers with little experience in bioinformatics to get meaningful information from Vibrio genomes with ease. We have tested the validity and suitability of these tools and features for use in the next-generation database development. PMID:25243218

  17. Assembly and annotation of full mitochondrial genomes for the corn rootworm species, Diabrotica virgifera virgifera and D. barberi (Insecta: Coleoptera: Chrysomelidae), using Next Generation Sequence data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complete mitochondrial genomes for two corn rootworm species, Diabrotica v. virgifera (16,747 bp) and D. barberi (16,632; Insecta: Coleoptera: Chrysomelidae), were assembled from Illumina HiSeq2000 read data. Annotation indicated that the order and orientation of 13 protein coding genes (PCGs), and...

  18. Efficient assembly and annotation of the transcriptome of catfish by RNA-seq analysis of a doubled haploid homozygote

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Upon the completion of whole genome sequencing, thorough genome annotation that associates genome sequences with biological meanings is essential. Genome annotation depends on the availability of transcript information as well as orthology information. In teleost fish, genome annotation is seriousl...

  19. Genome-Wide Functional Annotation of Human Protein-Coding Splice Variants Using Multiple Instance Learning.

    PubMed

    Panwar, Bharat; Menon, Rajasree; Eksi, Ridvan; Li, Hong-Dong; Omenn, Gilbert S; Guan, Yuanfang

    2016-06-01

    The vast majority of human multiexon genes undergo alternative splicing and produce a variety of splice variant transcripts and proteins, which can perform different functions. These protein-coding splice variants (PCSVs) greatly increase the functional diversity of proteins. Most functional annotation algorithms have been developed at the gene level; the lack of isoform-level gold standards is an important intellectual limitation for currently available machine learning algorithms. The accumulation of a large amount of RNA-seq data in the public domain greatly increases our ability to examine the functional annotation of genes at isoform level. In the present study, we used a multiple instance learning (MIL)-based approach for predicting the function of PCSVs. We used transcript-level expression values and gene-level functional associations from the Gene Ontology database. A support vector machine (SVM)-based 5-fold cross-validation technique was applied. Comparatively, genes with multiple PCSVs performed better than single PCSV genes, and performance also improved when more examples were available to train the models. We demonstrated our predictions using literature evidence of ADAM15, LMNA/C, and DMXL2 genes. All predictions have been implemented in a web resource called "IsoFunc", which is freely available for the global scientific community through http://guanlab.ccmb.med.umich.edu/isofunc . PMID:27142340

  20. KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome

    PubMed Central

    2013-01-01

    Background Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics. Description Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics. Conclusions We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of

  1. Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis

    PubMed Central

    Buisine, Nicolas; Ruan, Xiaoan; Bilesimo, Patrice; Grimaldi, Alexis; Alfama, Gladys; Ariyaratne, Pramila; Mulawadi, Fabianus; Chen, Jieqi; Sung, Wing-Kin; Liu, Edison T.; Demeneix, Barbara A.; Ruan, Yijun; Sachs, Laurent M.

    2015-01-01

    Genome-wide functional analyses require high-resolution genome assembly and annotation. We applied ChIA-PET to analyze gene regulatory networks, including 3D chromosome interactions, underlying thyroid hormone (TH) signaling in the frog Xenopus tropicalis. As the available versions of Xenopus tropicalis assembly and annotation lacked the resolution required for ChIA-PET we improve the genome assembly version 4.1 and annotations using data derived from the paired end tag (PET) sequencing technologies and approaches (e.g., DNA-PET [gPET], RNA-PET etc.). The large insert (~10Kb, ~17Kb) paired end DNA-PET with high throughput NGS sequencing not only significantly improved genome assembly quality, but also strongly reduced genome “fragmentation”, reducing total scaffold numbers by ~60%. Next, RNA-PET technology, designed and developed for the detection of full-length transcripts and fusion mRNA in whole transcriptome studies (ENCODE consortia), was applied to capture the 5' and 3' ends of transcripts. These amendments in assembly and annotation were essential prerequisites for the ChIA-PET analysis of TH transcription regulation. Their application revealed complex regulatory configurations of target genes and the structures of the regulatory networks underlying physiological responses. Our work allowed us to improve the quality of Xenopus tropicalis genomic resources, reaching the standard required for ChIA-PET analysis of transcriptional networks. We consider that the workflow proposed offers useful conceptual and methodological guidance and can readily be applied to other non-conventional models that have low-resolution genome data. PMID:26348928

  2. Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis.

    PubMed

    Buisine, Nicolas; Ruan, Xiaoan; Bilesimo, Patrice; Grimaldi, Alexis; Alfama, Gladys; Ariyaratne, Pramila; Mulawadi, Fabianus; Chen, Jieqi; Sung, Wing-Kin; Liu, Edison T; Demeneix, Barbara A; Ruan, Yijun; Sachs, Laurent M

    2015-01-01

    Genome-wide functional analyses require high-resolution genome assembly and annotation. We applied ChIA-PET to analyze gene regulatory networks, including 3D chromosome interactions, underlying thyroid hormone (TH) signaling in the frog Xenopus tropicalis. As the available versions of Xenopus tropicalis assembly and annotation lacked the resolution required for ChIA-PET we improve the genome assembly version 4.1 and annotations using data derived from the paired end tag (PET) sequencing technologies and approaches (e.g., DNA-PET [gPET], RNA-PET etc.). The large insert (~10 Kb, ~17 Kb) paired end DNA-PET with high throughput NGS sequencing not only significantly improved genome assembly quality, but also strongly reduced genome "fragmentation", reducing total scaffold numbers by ~60%. Next, RNA-PET technology, designed and developed for the detection of full-length transcripts and fusion mRNA in whole transcriptome studies (ENCODE consortia), was applied to capture the 5' and 3' ends of transcripts. These amendments in assembly and annotation were essential prerequisites for the ChIA-PET analysis of TH transcription regulation. Their application revealed complex regulatory configurations of target genes and the structures of the regulatory networks underlying physiological responses. Our work allowed us to improve the quality of Xenopus tropicalis genomic resources, reaching the standard required for ChIA-PET analysis of transcriptional networks. We consider that the workflow proposed offers useful conceptual and methodological guidance and can readily be applied to other non-conventional models that have low-resolution genome data. PMID:26348928

  3. Genome Annotation Provides Insight into Carbon Monoxide and Hydrogen Metabolism in Rubrivivax gelatinosus

    PubMed Central

    Wawrousek, Karen; Noble, Scott; Korlach, Jonas; Chen, Jin; Eckert, Carrie; Yu, Jianping; Maness, Pin-Ching

    2014-01-01

    We report here the sequencing and analysis of the genome of the purple non-sulfur photosynthetic bacterium Rubrivivax gelatinosus CBS. This microbe is a model for studies of its carboxydotrophic life style under anaerobic condition, based on its ability to utilize carbon monoxide (CO) as the sole carbon substrate and water as the electron acceptor, yielding CO2 and H2 as the end products. The CO-oxidation reaction is known to be catalyzed by two enzyme complexes, the CO dehydrogenase and hydrogenase. As expected, analysis of the genome of Rx. gelatinosus CBS reveals the presence of genes encoding both enzyme complexes. The CO-oxidation reaction is CO-inducible, which is consistent with the presence of two putative CO-sensing transcription factors in its genome. Genome analysis also reveals the presence of two additional hydrogenases, an uptake hydrogenase that liberates the electrons in H2 in support of cell growth, and a regulatory hydrogenase that senses H2 and relays the signal to a two-component system that ultimately controls synthesis of the uptake hydrogenase. The genome also contains two sets of hydrogenase maturation genes which are known to assemble the catalytic metallocluster of the hydrogenase NiFe active site. Collectively, the genome sequence and analysis information reveals the blueprint of an intricate network of signal transduction pathways and its underlying regulation that enables Rx. gelatinosus CBS to thrive on CO or H2 in support of cell growth. PMID:25479613

  4. Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data

    PubMed Central

    2011-01-01

    Background High-throughput sequencing is generating massive amounts of data at a pace that largely exceeds the throughput of data analysis routines. Here we introduce Fish the ChIPs (FC), a computational pipeline aimed at a broad public of users and designed to perform complete ChIP-Seq data analysis of an unlimited number of samples, thus increasing throughput, reproducibility and saving time. Results Starting from short read sequences, FC performs the following steps: 1) quality controls, 2) alignment to a reference genome, 3) peak calling, 4) genomic annotation, 5) generation of raw signal tracks for visualization on the UCSC and IGV genome browsers. FC exploits some of the fastest and most effective tools today available. Installation on a Mac platform requires very basic computational skills while configuration and usage are supported by a user-friendly graphic user interface. Alternatively, FC can be compiled from the source code on any Unix machine and then run with the possibility of customizing each single parameter through a simple configuration text file that can be generated using a dedicated user-friendly web-form. Considering the execution time, FC can be run on a desktop machine, even though the use of a computer cluster is recommended for analyses of large batches of data. FC is perfectly suited to work with data coming from Illumina Solexa Genome Analyzers or ABI SOLiD and its usage can potentially be extended to any sequencing platform. Conclusions Compared to existing tools, FC has two main advantages that make it suitable for a broad range of users. First of all, it can be installed and run by wet biologists on a Mac machine. Besides it can handle an unlimited number of samples, being convenient for large analyses. In this context, computational biologists can increase reproducibility of their ChIP-Seq data analyses while saving time for downstream analyses. Reviewers This article was reviewed by Gavin Huttley, George Shpakovski and Sarah

  5. Next generation models for storage and representation of microbial biological annotation

    PubMed Central

    2010-01-01

    Background Traditional genome annotation systems were developed in a very different computing era, one where the World Wide Web was just emerging. Consequently, these systems are built as centralized black boxes focused on generating high quality annotation submissions to GenBank/EMBL supported by expert manual curation. The exponential growth of sequence data drives a growing need for increasingly higher quality and automatically generated annotation. Typical annotation pipelines utilize traditional database technologies, clustered computing resources, Perl, C, and UNIX file systems to process raw sequence data, identify genes, and predict and categorize gene function. These technologies tightly couple the annotation software system to hardware and third party software (e.g. relational database systems and schemas). This makes annotation systems hard to reproduce, inflexible to modification over time, difficult to assess, difficult to partition across multiple geographic sites, and difficult to understand for those who are not domain experts. These systems are not readily open to scrutiny and therefore not scientifically tractable. The advent of Semantic Web standards such as Resource Description Framework (RDF) and OWL Web Ontology Language (OWL) enables us to construct systems that address these challenges in a new comprehensive way. Results Here, we develop a framework for linking traditional data to OWL-based ontologies in genome annotation. We show how data standards can decouple hardware and third party software tools from annotation pipelines, thereby making annotation pipelines easier to reproduce and assess. An illustrative example shows how TURTLE (Terse RDF Triple Language) can be used as a human readable, but also semantically-aware, equivalent to GenBank/EMBL files. Conclusions The power of this approach lies in its ability to assemble annotation data from multiple databases across multiple locations into a representation that is understandable to

  6. Next Generation Models for Storage and Representation of Microbial Biological Annotation

    SciTech Connect

    Quest, Daniel J; Land, Miriam L; Brettin, Thomas S; Cottingham, Robert W

    2010-01-01

    Background Traditional genome annotation systems were developed in a very different computing era, one where the World Wide Web was just emerging. Consequently, these systems are built as centralized black boxes focused on generating high quality annotation submissions to GenBank/EMBL supported by expert manual curation. The exponential growth of sequence data drives a growing need for increasingly higher quality and automatically generated annotation. Typical annotation pipelines utilize traditional database technologies, clustered computing resources, Perl, C, and UNIX file systems to process raw sequence data, identify genes, and predict and categorize gene function. These technologies tightly couple the annotation software system to hardware and third party software (e.g. relational database systems and schemas). This makes annotation systems hard to reproduce, inflexible to modification over time, difficult to assess, difficult to partition across multiple geographic sites, and difficult to understand for those who are not domain experts. These systems are not readily open to scrutiny and therefore not scientifically tractable. The advent of Semantic Web standards such as Resource Description Framework (RDF) and OWL Web Ontology Language (OWL) enables us to construct systems that address these challenges in a new comprehensive way. Results Here, we develop a framework for linking traditional data to OWL-based ontologies in genome annotation. We show how data standards can decouple hardware and third party software tools from annotation pipelines, thereby making annotation pipelines easier to reproduce and assess. An illustrative example shows how TURTLE (Terse RDF Triple Language) can be used as a human readable, but also semantically-aware, equivalent to GenBank/EMBL files. Conclusions The power of this approach lies in its ability to assemble annotation data from multiple databases across multiple locations into a representation that is understandable to

  7. Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle

    PubMed Central

    Zacher, Benedikt; Lidschreiber, Michael; Cramer, Patrick; Gagneur, Julien; Tresch, Achim

    2014-01-01

    DNA replication, transcription and repair involve the recruitment of protein complexes that change their composition as they progress along the genome in a directed or strand-specific manner. Chromatin immunoprecipitation in conjunction with hidden Markov models (HMMs) has been instrumental in understanding these processes, as they segment the genome into discrete states that can be related to DNA-associated protein complexes. However, current HMM-based approaches are not able to assign forward or reverse direction to states or properly integrate strand-specific (e.g., RNA expression) with non-strand-specific (e.g., ChIP) data, which is indispensable to accurately characterize directed processes. To overcome these limitations, we introduce bidirectional HMMs which infer directed genomic states from occupancy profiles de novo. Application to RNA polymerase II-associated factors in yeast and chromatin modifications in human T cells recovers the majority of transcribed loci, reveals gene-specific variations in the yeast transcription cycle and indicates the existence of directed chromatin state patterns at transcribed, but not at repressed, regions in the human genome. In yeast, we identify 32 new transcribed loci, a regulated initiation–elongation transition, the absence of elongation factors Ctk1 and Paf1 from a class of genes, a distinct transcription mechanism for highly expressed genes and novel DNA sequence motifs associated with transcription termination. We anticipate bidirectional HMMs to significantly improve the analyses of genome-associated directed processes. PMID:25527639

  8. Genome annotation past, present, and future: how to define an ORF at each locus.

    PubMed

    Brent, Michael R

    2005-12-01

    Driven by competition, automation, and technology, the genomics community has far exceeded its ambition to sequence the human genome by 2005. By analyzing mammalian genomes, we have shed light on the history of our DNA sequence, determined that alternatively spliced RNAs and retroposed pseudogenes are incredibly abundant, and glimpsed the apparently huge number of non-coding RNAs that play significant roles in gene regulation. Ultimately, genome science is likely to provide comprehensive catalogs of these elements. However, the methods we have been using for most of the last 10 years will not yield even one complete open reading frame (ORF) for every gene--the first plateau on the long climb toward a comprehensive catalog. These strategies--sequencing randomly selected cDNA clones, aligning protein sequences identified in other organisms, sequencing more genomes, and manual curation--will have to be supplemented by large-scale amplification and sequencing of specific predicted mRNAs. The steady improvements in gene prediction that have occurred over the last 10 years have increased the efficacy of this approach and decreased its cost. In this Perspective, I review the state of gene prediction roughly 10 years ago, summarize the progress that has been made since, argue that the primary ORF identification methods we have relied on so far are inadequate, and recommend a path toward completing the Catalog of Protein Coding Genes, Version 1.0. PMID:16339376

  9. Partitioning heritability by functional annotation using genome-wide association summary statistics

    PubMed Central

    Finucane, Hilary K.; Bulik-Sullivan, Brendan; Gusev, Alexander; Trynka, Gosia; Reshef, Yakir; Loh, Po-Ru; Anttila, Verneri; Xu, Han; Zang, Chongzhi; Farh, Kyle; Ripke, Stephan; Day, Felix R.; Consortium, ReproGen; Purcell, Shaun; Stahl, Eli; Lindstrom, Sara; Perry, John R. B.; Okada, Yukinori; Raychaudhuri, Soumya; Daly, Mark; Patterson, Nick; Neale, Benjamin M.; Price, Alkes L.

    2015-01-01

    Recent work has demonstrated that some functional categories of the genome contribute disproportionately to the heritability of complex diseases. Here, we analyze a broad set of functional elements, including cell-type-specific elements, to estimate their polygenic contributions to heritability in genome-wide association studies (GWAS) of 17 complex diseases and traits with an average sample size of 73,599. To enable this analysis, we introduce a new method, stratified LD score regression, for partitioning heritability from GWAS summary statistics while accounting for linked markers. This new method is computationally tractable at very large sample sizes, and leverages genome-wide information. Our results include a large enrichment of heritability in conserved regions across many traits; a very large immunological disease-specific enrichment of heritability in FANTOM5 enhancers; and many cell-type-specific enrichments including significant enrichment of central nervous system cell types in body mass index, age at menarche, educational attainment, and smoking behavior. PMID:26414678

  10. Genome annotation provides insight into carbon monoxide and hydrogen metabolism in Rubrivivax gelatinosus

    DOE PAGESBeta

    Wawrousek, Karen; Noble, Scott; Korlach, Jonas; Chen, Jin; Eckert, Carrie; Yu, Jianping; Maness, Pin -Ching

    2014-12-05

    In this article, we report here the sequencing and analysis of the genome of the purple non-sulfur photosynthetic bacterium Rubrivivax gelatinosus CBS. This microbe is a model for studies of its carboxydotrophic life style under anaerobic condition, based on its ability to utilize carbon monoxide (CO) as the sole carbon substrate and water as the electron acceptor, yielding CO2 and H2 as the end products. The CO-oxidation reaction is known to be catalyzed by two enzyme complexes, the CO dehydrogenase and hydrogenase. As expected, analysis of the genome of Rx. gelatinosus CBS reveals the presence of genes encoding both enzymemore » complexes. The CO-oxidation reaction is CO-inducible, which is consistent with the presence of two putative CO-sensing transcription factors in its genome. Genome analysis also reveals the presence of two additional hydrogenases, an uptake hydrogenase that liberates the electrons in H2 in support of cell growth, and a regulatory hydrogenase that senses H2 and relays the signal to a two-component system that ultimately controls synthesis of the uptake hydrogenase. The genome also contains two sets of hydrogenase maturation genes which are known to assemble the catalytic metallocluster of the hydrogenase NiFe active site. Finally and collectively, the genome sequence and analysis information reveals the blueprint of an intricate network of signal transduction pathways and its underlying regulation that enables Rx. gelatinosus CBS to thrive on CO or H2 in support of cell growth.« less

  11. Whole genome sequences and annotation of Micrococcus luteus SUBG006, a novel phytopathogen of mango

    PubMed Central

    Rakhashiya, Purvi M.; Patel, Pooja P.; Thaker, Vrinda S.

    2015-01-01

    Actinobaceria, Micrococcus luteus SUBG006 was isolated from infected leaves of Mangifera indica L. vr. Nylon in Rajkot, (22.30°N, 70.78°E), Gujarat, India. The genome size is 3.86 Mb with G + C content of 69.80% and contains 112 rRNA sequences (5S, 16S and 23S). The whole genome sequencing has been deposited in DDBJ/EMBL/GenBank under the accession number JOKP00000000. PMID:26697318

  12. Whole genome sequences and annotation of Micrococcus luteus SUBG006, a novel phytopathogen of mango.

    PubMed

    Rakhashiya, Purvi M; Patel, Pooja P; Thaker, Vrinda S

    2015-12-01

    Actinobaceria, Micrococcus luteus SUBG006 was isolated from infected leaves of Mangifera indica L. vr. Nylon in Rajkot, (22.30°N, 70.78°E), Gujarat, India. The genome size is 3.86 Mb with G + C content of 69.80% and contains 112 rRNA sequences (5S, 16S and 23S). The whole genome sequencing has been deposited in DDBJ/EMBL/GenBank under the accession number JOKP00000000. PMID:26697318

  13. Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus nematophila Strain F1

    PubMed Central

    Lanois, Anne; Ogier, Jean-Claude; Gouzy, Jérome; Laroui, Christine; Rouy, Zoé; Givaudan, Alain

    2013-01-01

    We report the 4.3-Mb genome sequence of Xenorhabdus nematophila strain F1, a Gram-negative bacterium that is a symbiont of the entomopathogenic nematode Steinernema carpocapsae and pathogenic by direct injection for a wide variety of insects. PMID:23788541

  14. The Complete Genome Sequence and Updated Annotation of Desulfovibrio alaskensis G20

    SciTech Connect

    Hauser, Loren John; Wall, Judy D.; Brown, Steven D; Land, Miriam L; Bruce, David; Detter, J. Chris; Frank, Larimer; Goodwin, Lynne A.; Han, Cliff; Lapidus, Alla L.; Nolan, Matt; Palumbo, Anthony Vito; Pitluck, Samual; Keller, Kimberly L; Rapp-Giles, Barbara J; Price, Morgan N.; Lin, Monica; Tapia, Roxanne; Copeland, A; Cheng, Jan-Fang

    2011-01-01

    Desulfovibrio alaskensis G20 (formerly desulfuricans G20) is a Gram-negative mesophilic sulfate-reducing bacterium (SRB), known to corrode ferrous metals and to reduce toxic radionuclides and metals such as uranium and chromium to sparingly soluble and less toxic forms. We present the 3.7 Mb genome sequence to provide insights into its physiology.

  15. Functional annotation of rare gene aberration drivers of pancreatic cancer | Office of Cancer Genomics

    Cancer.gov

    As we enter the era of precision medicine, characterization of cancer genomes will directly influence therapeutic decisions in the clinic. Here we describe a platform enabling functionalization of rare gene mutations through their high-throughput construction, molecular barcoding and delivery to cancer models for in vivo tumour driver screens. We apply these technologies to identify oncogenic drivers of pancreatic ductal adenocarcinoma (PDAC).

  16. Complete Genome Sequence and Updated Annotation of Desulfovibrio alaskensis G20

    DOE PAGESBeta

    Hauser, Loren J.; Land, Miriam L.; Brown, Steven D.; Larimer, Frank L; Keller, Kimberly L.; Rapp-Giles, Barbara J.; Price, Morgan N.; Lin, Monica A.; Bruce, David C.; Detter, John C.; et al

    2011-06-17

    Desulfovibrio alaskensis G20 (formerly desulfuricans G20) is a Gram-negative mesophilic sulfate-reducing bacterium (SRB), known to corrode ferrous metals and to reduce toxic radionuclides and metals such as uranium and chromium to sparingly soluble and less toxic forms. We present the 3.7 Mb genome sequence to provide insights into its physiology.

  17. Mapping and annotating obesity-related genes in pig and human genomes.

    PubMed

    Martelli, Pier Luigi; Fontanesi, Luca; Piovesan, Damiano; Fariselli, Piero; Casadio, Rita

    2014-01-01

    Background. Obesity is a major health problem in both developed and emerging countries. Obesity is a complex disease whose etiology involves genetic factors in strong interplay with environmental determinants and lifestyle. The discovery of genetic factors and biological pathways underlying human obesity is hampered by the difficulty in controlling the genetic background of human cohorts. Animal models are then necessary to further dissect the genetics of obesity. Pig has emerged as one of the most attractive models, because of the similarity with humans in the mechanisms regulating the fat deposition. Results. We collected the genes related to obesity in humans and to fat deposition traits in pig. We localized them on both human and pig genomes, building a map useful to interpret comparative studies on obesity. We characterized the collected genes structurally and functionally with BAR+ and mapped them on KEGG pathways and on STRING protein interaction network. Conclusions. The collected set consists of 361 obesity related genes in human and pig genomes. All genes were mapped on the human genome, and 54 could not be localized on the pig genome (release 2012). Only for 3 human genes there is no counterpart in pig, confirming that this animal is a good model for human obesity studies. Obesity related genes are mostly involved in regulation and signaling processes/pathways and relevant connection emerges between obesity-related genes and diseases such as cancer and infectious diseases. PMID:23855670

  18. Genome sequence and annotation of Trichoderma parareesei, the ancestor of the cellulase producer Trichoderma reesei

    DOE PAGESBeta

    Yang, Dongqing; Pomraning, Kyle; Kopchinskiy, Alexey; Karimi, Aghcheh Razieh; Atanasova, Lea; Chenthamara, Komal; Baker, Scott E.; Zhang, Ruifu; Shen, Qirong; Freitag, Michael; et al

    2015-08-13

    The filamentous fungus Trichoderma parareesei is the asexually reproducing ancestor of Trichoderma reesei, the holomorphic industrial producer of cellulase and hemicellulase. Here, we present the genome sequence of the T. parareesei type strain CBS 125925, which contains genes for 9,318 proteins.

  19. Genomic Resources for Gene Discovery, Functional Genome Annotation, and Evolutionary Studies of Maize and Its Close Relatives

    PubMed Central

    Wang, Chao; Shi, Xue; Liu, Lin; Li, Haiyan; Ammiraju, Jetty S.S.; Kudrna, David A.; Xiong, Wentao; Wang, Hao; Dai, Zhaozhao; Zheng, Yonglian; Lai, Jinsheng; Jin, Weiwei; Messing, Joachim; Bennetzen, Jeffrey L; Wing, Rod A.; Luo, Meizhong

    2013-01-01

    Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics. PMID:24037269

  20. Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions.

    PubMed

    Han, Ying; Hazelett, Dennis J; Wiklund, Fredrik; Schumacher, Fredrick R; Stram, Daniel O; Berndt, Sonja I; Wang, Zhaoming; Rand, Kristin A; Hoover, Robert N; Machiela, Mitchell J; Yeager, Merideth; Burdette, Laurie; Chung, Charles C; Hutchinson, Amy; Yu, Kai; Xu, Jianfeng; Travis, Ruth C; Key, Timothy J; Siddiq, Afshan; Canzian, Federico; Takahashi, Atsushi; Kubo, Michiaki; Stanford, Janet L; Kolb, Suzanne; Gapstur, Susan M; Diver, W Ryan; Stevens, Victoria L; Strom, Sara S; Pettaway, Curtis A; Al Olama, Ali Amin; Kote-Jarai, Zsofia; Eeles, Rosalind A; Yeboah, Edward D; Tettey, Yao; Biritwum, Richard B; Adjei, Andrew A; Tay, Evelyn; Truelove, Ann; Niwa, Shelley; Chokkalingam, Anand P; Isaacs, William B; Chen, Constance; Lindstrom, Sara; Le Marchand, Loic; Giovannucci, Edward L; Pomerantz, Mark; Long, Henry; Li, Fugen; Ma, Jing; Stampfer, Meir; John, Esther M; Ingles, Sue A; Kittles, Rick A; Murphy, Adam B; Blot, William J; Signorello, Lisa B; Zheng, Wei; Albanes, Demetrius; Virtamo, Jarmo; Weinstein, Stephanie; Nemesure, Barbara; Carpten, John; Leske, M Cristina; Wu, Suh-Yuh; Hennis, Anselm J M; Rybicki, Benjamin A; Neslund-Dudas, Christine; Hsing, Ann W; Chu, Lisa; Goodman, Phyllis J; Klein, Eric A; Zheng, S Lilly; Witte, John S; Casey, Graham; Riboli, Elio; Li, Qiyuan; Freedman, Matthew L; Hunter, David J; Gronberg, Henrik; Cook, Michael B; Nakagawa, Hidewaki; Kraft, Peter; Chanock, Stephen J; Easton, Douglas F; Henderson, Brian E; Coetzee, Gerhard A; Conti, David V; Haiman, Christopher A

    2015-10-01

    Interpretation of biological mechanisms underlying genetic risk associations for prostate cancer is complicated by the relatively large number of risk variants (n = 100) and the thousands of surrogate SNPs in linkage disequilibrium. Here, we combined three distinct approaches: multiethnic fine-mapping, putative functional annotation (based upon epigenetic data and genome-encoded features), and expression quantitative trait loci (eQTL) analyses, in an attempt to reduce this complexity. We examined 67 risk regions using genotyping and imputation-based fine-mapping in populations of European (cases/controls: 8600/6946), African (cases/controls: 5327/5136), Japanese (cases/controls: 2563/4391) and Latino (cases/controls: 1034/1046) ancestry. Markers at 55 regions passed a region-specific significance threshold (P-value cutoff range: 3.9 × 10(-4)-5.6 × 10(-3)) and in 30 regions we identified markers that were more significantly associated with risk than the previously reported variants in the multiethnic sample. Novel secondary signals (P < 5.0 × 10(-6)) were also detected in two regions (rs13062436/3q21 and rs17181170/3p12). Among 666 variants in the 55 regions with P-values within one order of magnitude of the most-associated marker, 193 variants (29%) in 48 regions overlapped with epigenetic or other putative functional marks. In 11 of the 55 regions, cis-eQTLs were detected with nearby genes. For 12 of the 55 regions (22%), the most significant region-specific, prostate-cancer associated variant represented the strongest candidate functional variant based on our annotations; the number of regions increased to 20 (36%) and 27 (49%) when examining the 2 and 3 most significantly associated variants in each region, respectively. These results have prioritized subsets of candidate variants for downstream functional evaluation. PMID:26162851

  1. Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics.

    PubMed

    Lundby, Alicia; Rossin, Elizabeth J; Steffensen, Annette B; Acha, Moshe Rav; Newton-Cheh, Christopher; Pfeufer, Arne; Lynch, Stacey N; Olesen, Søren-Peter; Brunak, Søren; Ellinor, Patrick T; Jukema, J Wouter; Trompet, Stella; Ford, Ian; Macfarlane, Peter W; Krijthe, Bouwe P; Hofman, Albert; Uitterlinden, André G; Stricker, Bruno H; Nathoe, Hendrik M; Spiering, Wilko; Daly, Mark J; Asselbergs, Folkert W; van der Harst, Pim; Milan, David J; de Bakker, Paul I W; Lage, Kasper; Olsen, Jesper V

    2014-08-01

    Genome-wide association studies (GWAS) have identified thousands of loci associated with complex traits, but it is challenging to pinpoint causal genes in these loci and to exploit subtle association signals. We used tissue-specific quantitative interaction proteomics to map a network of five genes involved in the Mendelian disorder long QT syndrome (LQTS). We integrated the LQTS network with GWAS loci from the corresponding common complex trait, QT-interval variation, to identify candidate genes that were subsequently confirmed in Xenopus laevis oocytes and zebrafish. We used the LQTS protein network to filter weak GWAS signals by identifying single-nucleotide polymorphisms (SNPs) in proximity to genes in the network supported by strong proteomic evidence. Three SNPs passing this filter reached genome-wide significance after replication genotyping. Overall, we present a general strategy to propose candidates in GWAS loci for functional studies and to systematically filter subtle association signals using tissue-specific quantitative interaction proteomics. PMID:24952909

  2. Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics

    PubMed Central

    Lundby, Alicia; Rossin, Elizabeth J.; Steffensen, Annette B.; Rav Acha, Moshe; Newton-Cheh, Christopher; Pfeufer, Arne; Lynch, Stacey N.; Olesen, Søren-Peter; Brunak, Søren; Ellinor, Patrick T.; Jukema, J.Wouter; Trompet, Stella; Ford, Ian; Macfarlane, Peter W.; Krijthe, Bouwe P.; Hofman, Albert; Uitterlinden, Andre G.; Stricker, Bruno H.; Nathoe, Hendrik M.; Spiering, Wilko; Daly, Mark J.; Asselbergs, Folkert W.; van der Harst, Pim; Milan, David J.; de Bakker, Paul I.W.; Lage, Kasper; Olsen, Jesper V.

    2014-01-01

    Genome-wide association studies (GWAS) have identified thousands of loci associated wtih complex traits, but it is challenging to pinpoint causal genes in these loci and to exploit subtle association signals. We used tissue-specific quantitative interaction proteomics to map a network of five genes involved in the Mendelian disorder long QT syndrome (LQTS). We integrated the LQTS network with GWAS loci from the corresponding common complex trait, QT interval variation, to identify candidate genes that were subsequently confirmed in Xenopus laevis oocytes and zebrafish. We used the LQTS protein network to filter weak GWAS signals by identifying single nucleotide polymorphisms (SNPs) in proximity to genes in the network supported by strong proteomic evidence. Three SNPs passing this filter reached genome-wide significance after replication genotyping. Overall, we present a general strategy to propose candidates in GWAS loci for functional studies and to systematically filter subtle association signals using tissue-specific quantitative interaction proteomics. PMID:24952909

  3. Community gene annotation in practice

    PubMed Central

    Loveland, Jane E.; Gilbert, James G.R.; Griffiths, Ed; Harrow, Jennifer L.

    2012-01-01

    Manual annotation of genomic data is extremely valuable to produce an accurate reference gene set but is expensive compared with automatic methods and so has been limited to model organisms. Annotation tools that have been developed at the Wellcome Trust Sanger Institute (WTSI, http://www.sanger.ac.uk/.) are being used to fill that gap, as they can be used remotely and so open up viable community annotation collaborations. We introduce the ‘Blessed’ annotator and ‘Gatekeeper’ approach to Community Annotation using the Otterlace/ZMap genome annotation tool. We also describe the strategies adopted for annotation consistency, quality control and viewing of the annotation. Database URL: http://vega.sanger.ac.uk/index.html PMID:22434843

  4. Complete Genome Sequence and Annotation of Corynebacterium singulare DSM 44357, Isolated from a Human Semen Specimen

    PubMed Central

    Merten, Madlen; Brinkrolf, Karina; Albersmeier, Andreas; Kutter, Yvonne; Rückert, Christian

    2015-01-01

    Corynebacterium singulare DSM 44357 is a urease-positive microorganism isolated from human semen. The complete genome sequence of C. singulare DSM 44357 comprises 2,830,519 bp with a mean G+C content of 60.12% and 2,581 protein-coding genes. The deduced antibiotic resistance pattern of this strain includes macrolides, lincosamides, aminoglycosides, chloramphenicol, and tetracyline. PMID:25814602

  5. Partitioning heritability by functional annotation using genome-wide association summary statistics.

    PubMed

    Finucane, Hilary K; Bulik-Sullivan, Brendan; Gusev, Alexander; Trynka, Gosia; Reshef, Yakir; Loh, Po-Ru; Anttila, Verneri; Xu, Han; Zang, Chongzhi; Farh, Kyle; Ripke, Stephan; Day, Felix R; Purcell, Shaun; Stahl, Eli; Lindstrom, Sara; Perry, John R B; Okada, Yukinori; Raychaudhuri, Soumya; Daly, Mark J; Patterson, Nick; Neale, Benjamin M; Price, Alkes L

    2015-11-01

    Recent work has demonstrated that some functional categories of the genome contribute disproportionately to the heritability of complex diseases. Here we analyze a broad set of functional elements, including cell type-specific elements, to estimate their polygenic contributions to heritability in genome-wide association studies (GWAS) of 17 complex diseases and traits with an average sample size of 73,599. To enable this analysis, we introduce a new method, stratified LD score regression, for partitioning heritability from GWAS summary statistics while accounting for linked markers. This new method is computationally tractable at very large sample sizes and leverages genome-wide information. Our findings include a large enrichment of heritability in conserved regions across many traits, a very large immunological disease-specific enrichment of heritability in FANTOM5 enhancers and many cell type-specific enrichments, including significant enrichment of central nervous system cell types in the heritability of body mass index, age at menarche, educational attainment and smoking behavior. PMID:26414678

  6. Annotation of additional evolutionary conserved microRNAs in CHO cells from updated genomic data

    PubMed Central

    Hackl, Matthias; Klanert, Gerald; Jadhav, Vaibhav; Reithofer, Manuel; Stiefel, Fabian; Hesse, Friedemann; Grillari, Johannes; Borth, Nicole

    2015-01-01

    ABSTRACT MicroRNAs are small non‐coding RNAs that play a critical role in post‐transcriptional control of gene expression. Recent publications of genomic sequencing data from the Chinese Hamster (CGR) and Chinese hamster ovary (CHO) cells provide new tools for the discovery of novel miRNAs in this important production system. Version 20 of the miRNA registry miRBase contains 307 mature miRNAs and 200 precursor sequences for CGR/CHO. We searched for evolutionary conserved miRNAs from miRBase v20 in recently published genomic data, derived from Chinese hamster and CHO cells, to further extend the list of known miRNAs. With our approach we could identify several hundred miRNA sequences in the genome. For several of these, the expression in CHO cells could be verified from multiple next‐generation sequencing experiments. In addition, several hundred unexpressed miRNAs are awaiting further confirmation by testing for their transcription in different Chinese hamster tissues. Biotechnol. Bioeng. 2015;112: 1488–1493. © 2015 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc. PMID:25689160

  7. GRAIL and GenQuest Sequence Annotation Tools

    SciTech Connect

    Xu, Ying; Shah, Manesh B.; Einstein, J. Ralph; Parang, Morey; Snoddy, Jay; Petrov, Sergey; Olman, Victor; Zhang, Ge; Mural, Richard J.; Uberbacher, Edward C.

    1997-12-31

    Our goal is to develop and implement an integrated intelligent system which can recognize biologically significant features in DNA sequence and provide insight into the organization and function of regions of genomic DNA. GRAIL is a modular expert system which facilitates the recognition of gene features and provides an environment for the construction of sequence annotation. The last several years have seen a rapid evolution of the technology for analyzing genomic DNA sequences. The current GRAIL systems (including the e-mail, XGRAIL, JAVA-GRAIL and genQuest systems) are perhaps the most widely used, comprehensive, and user friendly systems available for computational characterization of genomic DNA sequence.

  8. Functional Annotation, Genome Organization and Phylogeny of the Grapevine (Vitis vinifera) Terpene Synthase Gene Family Based on Genome Assembly, FLcDNA Cloning, and Enzyme Assays

    PubMed Central

    2010-01-01

    Background Terpenoids are among the most important constituents of grape flavour and wine bouquet, and serve as useful metabolite markers in viticulture and enology. Based on the initial 8-fold sequencing of a nearly homozygous Pinot noir inbred line, 89 putative terpenoid synthase genes (VvTPS) were predicted by in silico analysis of the grapevine (Vitis vinifera) genome assembly [1]. The finding of this very large VvTPS family, combined with the importance of terpenoid metabolism for the organoleptic properties of grapevine berries and finished wines, prompted a detailed examination of this gene family at the genomic level as well as an investigation into VvTPS biochemical functions. Results We present findings from the analysis of the up-dated 12-fold sequencing and assembly of the grapevine genome that place the number of predicted VvTPS genes at 69 putatively functional VvTPS, 20 partial VvTPS, and 63 VvTPS probable pseudogenes. Gene discovery and annotation included information about gene architecture and chromosomal location. A dense cluster of 45 VvTPS is localized on chromosome 18. Extensive FLcDNA cloning, gene synthesis, and protein expression enabled functional characterization of 39 VvTPS; this is the largest number of functionally characterized TPS for any species reported to date. Of these enzymes, 23 have unique functions and/or phylogenetic locations within the plant TPS gene family. Phylogenetic analyses of the TPS gene family showed that while most VvTPS form species-specific gene clusters, there are several examples of gene orthology with TPS of other plant species, representing perhaps more ancient VvTPS, which have maintained functions independent of speciation. Conclusions The highly expanded VvTPS gene family underpins the prominence of terpenoid metabolism in grapevine. We provide a detailed experimental functional annotation of 39 members of this important gene family in grapevine and comprehensive information about gene structure and

  9. Comparisons of Shewanella strains based on genome annotations, modeling and experiments

    SciTech Connect

    Ong, Wai Kit; Vu, Trang; Lovendahl, Klaus N.; Llull, Jenna; Serres, Margaret; Romine, Margaret F.; Reed, Jennifer L.

    2014-01-01

    Shewanella is a genus of facultatively anaerobic, Gram-negative bacteria that have highly adaptable metabolism which allows them to thrive in diverse environments. This quality makes them attractive target bacteria for research in bioremediation and microbial fuel cell applications. Constraint-based modeling is a useful tool for helping researchers gain insights into the metabolic capabilities of these bacteria. However, Shewanella oneidensis MR-1 is the only strain with a genome-scale metabolic model constructed out of the 22 sequenced Shewanella strains.

  10. BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments

    PubMed Central

    Al-Shahrour, Fátima; Minguez, Pablo; Tárraga, Joaquín; Montaner, David; Alloza, Eva; Vaquerizas, Juan M.; Conde, Lucía; Blaschke, Christian; Vera, Javier; Dopazo, Joaquín

    2006-01-01

    We present a new version of Babelomics, a complete suite of web tools for functional analysis of genome-scale experiments, with new and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An improved indexing has considerably speeded up several of the modules. An improved version of the FatiScan method for studying the coordinate behaviour of groups of functionally related genes is presented, along with a similar tool, the Gene Set Enrichment Analysis. Babelomics is now more oriented to test systems biology inspired hypotheses. Babelomics can be found at . PMID:16845052

  11. Protein surface analysis for function annotation in high-throughput structural genomics pipeline

    PubMed Central

    Binkowski, T. Andrew; Joachimiak, Andrzej; Liang, Jie

    2005-01-01

    Structural genomics (SG) initiatives are expanding the universe of protein fold space by rapidly determining structures of proteins that were intentionally selected on the basis of low sequence similarity to proteins of known structure. Often these proteins have no associated biochemical or cellular functions. The SG success has resulted in an accelerated deposition of novel structures. In some cases the structural bioinformatics analysis applied to these novel structures has provided specific functional assignment. However, this approach has also uncovered limitations in the functional analysis of uncharacterized proteins using traditional sequence and backbone structure methodologies. A novel method, named pvSOAR (pocket and void Surface of Amino Acid Residues), of comparing the protein surfaces of geometrically defined pockets and voids was developed. pvSOAR was able to detect previously unrecognized and novel functional relationships between surface features of proteins. In this study, pvSOAR is applied to several structural genomics proteins. We examined the surfaces of YecM, BioH, and RpiB from Escherichia coli as well as the CBS domains from inosine-5′-monosphate dehydrogenase from Streptococcus pyogenes, conserved hypothetical protein Ta549 from Thermoplasm acidophilum, and CBS domain protein mt1622 from Methanobacterium thermoautotrophicum with the goal to infer information about their biochemical function. PMID:16322579

  12. GELBANK : A database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes.

    SciTech Connect

    Babnigg, G.; Giometti, C. S.; Biosciences Division

    2004-01-01

    GELBANK is a publicly available database of two-dimensional gel electrophoresis (2DE) gel patterns of proteomes from organisms with known genome information (available at and ftp://bioinformatics.anl.gov/gelbank/). Currently it includes 131 completed, mostly microbial proteomes available from the National Center for Biotechnology Information. A web interface allows the upload of 2D gel patterns and their annotation for registered users. The images are organized by species, tissue type, separation method, sample type and staining method. The database can be queried based on protein or 2DE-pattern attributes. A web interface allows registered users to assign molecular weight and pH gradient profiles to their own 2D gel patterns as well as to link protein identifications to a given spot on the pattern. The website presents all of the submitted 2D gel patterns where the end-user can dynamically display the images or parts of images along with molecular weight, pH profile information and linked protein identification. A collection of images can be selected for the creation of animations from which the user can select sub-regions of interest and unlimited 2D gel patterns for visualization. The website currently presents 233 identifications for 81 gel patterns for Homo sapiens, Methanococcus jannaschii, Pyro coccus furiosus, Shewanella oneidensis, Escherichia coli and Deinococcus radiodurans.

  13. Integrative bioinformatics for functional genome annotation: trawling for G protein-coupled receptors.

    PubMed

    Flower, Darren R; Attwood, Teresa K

    2004-12-01

    G protein-coupled receptors (GPCR) are amongst the best studied and most functionally diverse types of cell-surface protein. The importance of GPCRs as mediates or cell function and organismal developmental underlies their involvement in key physiological roles and their prominence as targets for pharmacological therapeutics. In this review, we highlight the requirement for integrated protocols which underline the different perspectives offered by different sequence analysis methods. BLAST and FastA offer broad brush strokes. Motif-based search methods add the fine detail. Structural modelling offers another perspective which allows us to elucidate the physicochemical properties that underlie ligand binding. Together, these different views provide a more informative and a more detailed picture of GPCR structure and function. Many GPCRs remain orphan receptors with no identified ligand, yet as computer-driven functional genomics starts to elaborate their functions, a new understanding of their roles in cell and developmental biology will follow. PMID:15561589

  14. Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements

    PubMed Central

    Jühling, Frank; Pütz, Joern; Bernt, Matthias; Donath, Alexander; Middendorf, Martin; Florentz, Catherine; Stadler, Peter F.

    2012-01-01

    Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit ‘bizarre’ secondary structures, lacking complete domains of the common cloverleaf. Such sequences are hard to detect and hence frequently missed in computational analyses and mitochondrial genome annotation. Here, we introduce an automatic annotation procedure for mitochondrial tRNA genes in Metazoa based on sequence and structural information in manually curated covariance models. The method, applied to re-annotate 1876 available metazoan mitochondrial RefSeq genomes, allows to distinguish between remaining functional genes and degrading ‘pseudogenes’, even at early stages of divergence. The subsequent analysis of a comprehensive set of mitochondrial tRNA genes gives new insights into the evolution of structures of mitochondrial tRNA sequences as well as into the mechanisms of genome rearrangements. We find frequent losses of tRNA genes concentrated in basal Metazoa, frequent independent losses of individual parts of tRNA genes, particularly in Arthropoda, and wide-spread conserved overlaps of tRNAs in opposite reading direction. Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders. PMID:22139921

  15. Sma3s: A Three-Step Modular Annotator for Large Sequence Datasets

    PubMed Central

    Muñoz-Mérida, Antonio; Viguera, Enrique; Claros, M. Gonzalo; Trelles, Oswaldo; Pérez-Pulido, Antonio J.

    2014-01-01

    Automatic sequence annotation is an essential component of modern ‘omics’ studies, which aim to extract information from large collections of sequence data. Most existing tools use sequence homology to establish evolutionary relationships and assign putative functions to sequences. However, it can be difficult to define a similarity threshold that achieves sufficient coverage without sacrificing annotation quality. Defining the correct configuration is critical and can be challenging for non-specialist users. Thus, the development of robust automatic annotation techniques that generate high-quality annotations without needing expert knowledge would be very valuable for the research community. We present Sma3s, a tool for automatically annotating very large collections of biological sequences from any kind of gene library or genome. Sma3s is composed of three modules that progressively annotate query sequences using either: (i) very similar homologues, (ii) orthologous sequences or (iii) terms enriched in groups of homologous sequences. We trained the system using several random sets of known sequences, demonstrating average sensitivity and specificity values of ∼85%. In conclusion, Sma3s is a versatile tool for high-throughput annotation of a wide variety of sequence datasets that outperforms the accuracy of other well-established annotation algorithms, and it can enrich existing database annotations and uncover previously hidden features. Importantly, Sma3s has already been used in the functional annotation of two published transcriptomes. PMID:24501397

  16. Sma3s: a three-step modular annotator for large sequence datasets.

    PubMed

    Muñoz-Mérida, Antonio; Viguera, Enrique; Claros, M Gonzalo; Trelles, Oswaldo; Pérez-Pulido, Antonio J

    2014-08-01

    Automatic sequence annotation is an essential component of modern 'omics' studies, which aim to extract information from large collections of sequence data. Most existing tools use sequence homology to establish evolutionary relationships and assign putative functions to sequences. However, it can be difficult to define a similarity threshold that achieves sufficient coverage without sacrificing annotation quality. Defining the correct configuration is critical and can be challenging for non-specialist users. Thus, the development of robust automatic annotation techniques that generate high-quality annotations without needing expert knowledge would be very valuable for the research community. We present Sma3s, a tool for automatically annotating very large collections of biological sequences from any kind of gene library or genome. Sma3s is composed of three modules that progressively annotate query sequences using either: (i) very similar homologues, (ii) orthologous sequences or (iii) terms enriched in groups of homologous sequences. We trained the system using several random sets of known sequences, demonstrating average sensitivity and specificity values of ~85%. In conclusion, Sma3s is a versatile tool for high-throughput annotation of a wide variety of sequence datasets that outperforms the accuracy of other well-established annotation algorithms, and it can enrich existing database annotations and uncover previously hidden features. Importantly, Sma3s has already been used in the functional annotation of two published transcriptomes. PMID:24501397

  17. Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.

    PubMed

    Gaulton, Kyle J; Ferreira, Teresa; Lee, Yeji; Raimondo, Anne; Mägi, Reedik; Reschen, Michael E; Mahajan, Anubha; Locke, Adam; Rayner, N William; Robertson, Neil; Scott, Robert A; Prokopenko, Inga; Scott, Laura J; Green, Todd; Sparso, Thomas; Thuillier, Dorothee; Yengo, Loic; Grallert, Harald; Wahl, Simone; Frånberg, Mattias; Strawbridge, Rona J; Kestler, Hans; Chheda, Himanshu; Eisele, Lewin; Gustafsson, Stefan; Steinthorsdottir, Valgerdur; Thorleifsson, Gudmar; Qi, Lu; Karssen, Lennart C; van Leeuwen, Elisabeth M; Willems, Sara M; Li, Man; Chen, Han; Fuchsberger, Christian; Kwan, Phoenix; Ma, Clement; Linderman, Michael; Lu, Yingchang; Thomsen, Soren K; Rundle, Jana K; Beer, Nicola L; van de Bunt, Martijn; Chalisey, Anil; Kang, Hyun Min; Voight, Benjamin F; Abecasis, Gonçalo R; Almgren, Peter; Baldassarre, Damiano; Balkau, Beverley; Benediktsson, Rafn; Blüher, Matthias; Boeing, Heiner; Bonnycastle, Lori L; Bottinger, Erwin P; Burtt, Noël P; Carey, Jason; Charpentier, Guillaume; Chines, Peter S; Cornelis, Marilyn C; Couper, David J; Crenshaw, Andrew T; van Dam, Rob M; Doney, Alex S F; Dorkhan, Mozhgan; Edkins, Sarah; Eriksson, Johan G; Esko, Tonu; Eury, Elodie; Fadista, João; Flannick, Jason; Fontanillas, Pierre; Fox, Caroline; Franks, Paul W; Gertow, Karl; Gieger, Christian; Gigante, Bruna; Gottesman, Omri; Grant, George B; Grarup, Niels; Groves, Christopher J; Hassinen, Maija; Have, Christian T; Herder, Christian; Holmen, Oddgeir L; Hreidarsson, Astradur B; Humphries, Steve E; Hunter, David J; Jackson, Anne U; Jonsson, Anna; Jørgensen, Marit E; Jørgensen, Torben; Kao, Wen-Hong L; Kerrison, Nicola D; Kinnunen, Leena; Klopp, Norman; Kong, Augustine; Kovacs, Peter; Kraft, Peter; Kravic, Jasmina; Langford, Cordelia; Leander, Karin; Liang, Liming; Lichtner, Peter; Lindgren, Cecilia M; Lindholm, Eero; Linneberg, Allan; Liu, Ching-Ti; Lobbens, Stéphane; Luan, Jian'an; Lyssenko, Valeriya; Männistö, Satu; McLeod, Olga; Meyer, Julia; Mihailov, Evelin; Mirza, Ghazala; Mühleisen, Thomas W; Müller-Nurasyid, Martina; Navarro, Carmen; Nöthen, Markus M; Oskolkov, Nikolay N; Owen, Katharine R; Palli, Domenico; Pechlivanis, Sonali; Peltonen, Leena; Perry, John R B; Platou, Carl G P; Roden, Michael; Ruderfer, Douglas; Rybin, Denis; van der Schouw, Yvonne T; Sennblad, Bengt; Sigurðsson, Gunnar; Stančáková, Alena; Steinbach, Gerald; Storm, Petter; Strauch, Konstantin; Stringham, Heather M; Sun, Qi; Thorand, Barbara; Tikkanen, Emmi; Tonjes, Anke; Trakalo, Joseph; Tremoli, Elena; Tuomi, Tiinamaija; Wennauer, Roman; Wiltshire, Steven; Wood, Andrew R; Zeggini, Eleftheria; Dunham, Ian; Birney, Ewan; Pasquali, Lorenzo; Ferrer, Jorge; Loos, Ruth J F; Dupuis, Josée; Florez, Jose C; Boerwinkle, Eric; Pankow, James S; van Duijn, Cornelia; Sijbrands, Eric; Meigs, James B; Hu, Frank B; Thorsteinsdottir, Unnur; Stefansson, Kari; Lakka, Timo A; Rauramaa, Rainer; Stumvoll, Michael; Pedersen, Nancy L; Lind, Lars; Keinanen-Kiukaanniemi, Sirkka M; Korpi-Hyövälti, Eeva; Saaristo, Timo E; Saltevo, Juha; Kuusisto, Johanna; Laakso, Markku; Metspalu, Andres; Erbel, Raimund; Jöcke, Karl-Heinz; Moebus, Susanne; Ripatti, Samuli; Salomaa, Veikko; Ingelsson, Erik; Boehm, Bernhard O; Bergman, Richard N; Collins, Francis S; Mohlke, Karen L; Koistinen, Heikki; Tuomilehto, Jaakko; Hveem, Kristian; Njølstad, Inger; Deloukas, Panagiotis; Donnelly, Peter J; Frayling, Timothy M; Hattersley, Andrew T; de Faire, Ulf; Hamsten, Anders; Illig, Thomas; Peters, Annette; Cauchi, Stephane; Sladek, Rob; Froguel, Philippe; Hansen, Torben; Pedersen, Oluf; Morris, Andrew D; Palmer, Collin N A; Kathiresan, Sekar; Melander, Olle; Nilsson, Peter M; Groop, Leif C; Barroso, Inês; Langenberg, Claudia; Wareham, Nicholas J; O'Callaghan, Christopher A; Gloyn, Anna L; Altshuler, David; Boehnke, Michael; Teslovich, Tanya M; McCarthy, Mark I; Morris, Andrew P

    2015-12-01

    We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease. PMID:26551672

  18. CrAgDb--a database of annotated chaperone repertoire in archaeal genomes.

    PubMed

    Rani, Shikha; Srivastava, Abhishikha; Kumar, Manish; Goel, Manisha

    2016-03-01

    Chaperones are a diverse class of ubiquitous proteins that assist other cellular proteins in folding correctly and maintaining their native structure. Many different chaperones cooperate to constitute the 'proteostasis' machinery in the cells. It has been proposed earlier that archaeal organisms could be ideal model systems for deciphering the basic functioning of the 'protein folding machinery' in higher eukaryotes. Several chaperone families have been characterized in archaea over the years but mostly one protein at a time, making it difficult to decipher the composition and mechanistics of the protein folding system as a whole. In order to deal with these lacunae, we have developed a database of all archaeal chaperone proteins, CrAgDb (Chaperone repertoire in Archaeal genomes). The data have been presented in a systematic way with intuitive browse and search facilities for easy retrieval of information. Access to these curated datasets should expedite large-scale analysis of archaeal chaperone networks and significantly advance our understanding of operation and regulation of the protein folding machinery in archaea. Researchers could then translate this knowledge to comprehend the more complex protein folding pathways in eukaryotic systems. The database is freely available at http://14.139.227.92/mkumar/cragdb/. PMID:26862144

  19. Genetic fine-mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci

    PubMed Central

    Mahajan, Anubha; Locke, Adam; Rayner, N William; Robertson, Neil; Scott, Robert A; Prokopenko, Inga; Scott, Laura J; Green, Todd; Sparso, Thomas; Thuillier, Dorothee; Yengo, Loic; Grallert, Harald; Wahl, Simone; Frånberg, Mattias; Strawbridge, Rona J; Kestler, Hans; Chheda, Himanshu; Eisele, Lewin; Gustafsson, Stefan; Steinthorsdottir, Valgerdur; Thorleifsson, Gudmar; Qi, Lu; Karssen, Lennart C; van Leeuwen, Elisabeth M; Willems, Sara M; Li, Man; Chen, Han; Fuchsberger, Christian; Kwan, Phoenix; Ma, Clement; Linderman, Michael; Lu, Yingchang; Thomsen, Soren K; Rundle, Jana K; Beer, Nicola L; van de Bunt, Martijn; Chalisey, Anil; Kang, Hyun Min; Voight, Benjamin F; Abecasis, Goncalo R; Almgren, Peter; Baldassarre, Damiano; Balkau, Beverley; Benediktsson, Rafn; Blüher, Matthias; Boeing, Heiner; Bonnycastle, Lori L; Borringer, Erwin P; Burtt, Noël P; Carey, Jason; Charpentier, Guillaume; Chines, Peter S; Cornelis, Marilyn C; Couper, David J; Crenshaw, Andrew T; van Dam, Rob M; Doney, Alex SF; Dorkhan, Mozhgan; Edkins, Sarah; Eriksson, Johan G; Esko, Tonu; Eury, Elodie; Fadista, João; Flannick, Jason; Fontanillas, Pierre; Fox, Caroline; Franks, Paul W; Gertow, Karl; Gieger, Christian; Gigante, Bruna; Gottesman, Omri; Grant, George B; Grarup, Niels; Groves, Christopher J; Hassinen, Maija; Have, Christian T; Herder, Christian; Holmen, Oddgeir L; Hreidarsson, Astradur B; Humphries, Steve E; Hunter, David J; Jackson, Anne U; Jonsson, Anna; Jørgensen, Marit E; Jørgensen, Torben; Kerrison, Nicola D; Kinnunen, Leena; Klopp, Norman; Kong, Augustine; Kovacs, Peter; Kraft, Peter; Kravic, Jasmina; Langford, Cordelia; Leander, Karin; Liang, Liming; Lichtner, Peter; Lindgren, Cecilia M; Lindholm, Eero; Linneberg, Allan; Liu, Ching-Ti; Lobbens, Stéphane; Luan, Jian’an; Lyssenko, Valeriya; Männistö, Satu; McLeod, Olga; Meyer, Julia; Mihailov, Evelin; Mirza, Ghazala; Mühleisen, Thomas W; Müller-Nurasyid, Martina; Navarro, Carmen; Nöthen, Markus M; Oskolkov, Nikolay N; Owen, Katharine R; Palli, Domenico; Pechlivanis, Sonali; Perry, John RB; Platou, Carl GP; Roden, Michael; Ruderfer, Douglas; Rybin, Denis; van der Schouw, Yvonne T; Sennblad, Bengt; Sigurðsson, Gunnar; Stančáková, Alena; Steinbach, Gerald; Storm, Petter; Strauch, Konstantin; Stringham, Heather M; Sun, Qi; Thorand, Barbara; Tikkanen, Emmi; Tonjes, Anke; Trakalo, Joseph; Tremoli, Elena; Tuomi, Tiinamaija; Wennauer, Roman; Wood, Andrew R; Zeggini, Eleftheria; Dunham, Ian; Birney, Ewan; Pasquali, Lorenzo; Ferrer, Jorge; Loos, Ruth JF; Dupuis, Josée; Florez, Jose C; Boerwinkle, Eric; Pankow, James S; van Duijn, Cornelia; Sijbrands, Eric; Meigs, James B; Hu, Frank B; Thorsteinsdottir, Unnur; Stefansson, Kari; Lakka, Timo A; Rauramaa, Rainer; Stumvoll, Michael; Pedersen, Nancy L; Lind, Lars; Keinanen-Kiukaanniemi, Sirkka M; Korpi-Hyövälti, Eeva; Saaristo, Timo E; Saltevo, Juha; Kuusisto, Johanna; Laakso, Markku; Metspalu, Andres; Erbel, Raimund; Jöckel, Karl-Heinz; Moebus, Susanne; Ripatti, Samuli; Salomaa, Veikko; Ingelsson, Erik; Boehm, Bernhard O; Bergman, Richard N; Collins, Francis S; Mohlke, Karen L; Koistinen, Heikki; Tuomilehto, Jaakko; Hveem, Kristian; Njølstad, Inger; Deloukas, Panagiotis; Donnelly, Peter J; Frayling, Timothy M; Hattersley, Andrew T; de Faire, Ulf; Hamsten, Anders; Illig, Thomas; Peters, Annette; Cauchi, Stephane; Sladek, Rob; Froguel, Philippe; Hansen, Torben; Pedersen, Oluf; Morris, Andrew D; Palmer, Collin NA; Kathiresan, Sekar; Melander, Olle; Nilsson, Peter M; Groop, Leif C; Barroso, Inês; Langenberg, Claudia; Wareham, Nicholas J; O’Callaghan, Christopher A; Gloyn, Anna L; Altshuler, David; Boehnke, Michael; Teslovich, Tanya M; McCarthy, Mark I; Morris, Andrew P

    2015-01-01

    We performed fine-mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in/near KCNQ1. “Credible sets” of variants most likely to drive each distinct signal mapped predominantly to non-coding sequence, implying that T2D association is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine-mapping implicated rs10830963 as driving T2D association. We confirmed that this T2D-risk allele increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D-risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease. PMID:26551672

  20. Algal functional annotation tool

    Energy Science and Technology Software Center (ESTSC)

    2012-07-12

    Abstract BACKGROUND: Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations tomore » interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. DESCRIPTION: The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on

  1. Algal functional annotation tool

    SciTech Connect

    2012-07-12

    Abstract BACKGROUND: Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. DESCRIPTION: The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on KEGG

  2. An integrated pipeline for next generation sequencing and annotation of the complete mitochondrial genome of the giant intestinal fluke, Fasciolopsis buski (Lankester, 1857) Looss, 1899

    PubMed Central

    Biswal, Devendra Kumar; Ghatani, Sudeep; Shylla, Jollin A.; Sahu, Ranjana; Mullapudi, Nandita

    2013-01-01

    Helminths include both parasitic nematodes (roundworms) and platyhelminths (trematode and cestode flatworms) that are abundant, and are of clinical importance. The genetic characterization of parasitic flatworms using advanced molecular tools is central to the diagnosis and control of infections. Although the nuclear genome houses suitable genetic markers (e.g., in ribosomal (r) DNA) for species identification and molecular characterization, the mitochondrial (mt) genome consistently provides a rich source of novel markers for informative systematics and epidemiological studies. In the last decade, there have been some important advances in mtDNA genomics of helminths, especially lung flukes, liver flukes and intestinal flukes. Fasciolopsis buski, often called the giant intestinal fluke, is one of the largest digenean trematodes infecting humans and found primarily in Asia, in particular the Indian subcontinent. Next-generation sequencing (NGS) technologies now provide opportunities for high throughput sequencing, assembly and annotation within a short span of time. Herein, we describe a high-throughput sequencing and bioinformatics pipeline for mt genomics for F. buski that emphasizes the utility of short read NGS platforms such as Ion Torrent and Illumina in successfully sequencing and assembling the mt genome using innovative approaches for PCR primer design as well as assembly. We took advantage of our NGS whole genome sequence data (unpublished so far) for F. buski and its comparison with available data for the Fasciola hepatica mtDNA as the reference genome for design of precise and specific primers for amplification of mt genome sequences from F. buski. A long-range PCR was carried out to create an NGS library enriched in mt DNA sequences. Two different NGS platforms were employed for complete sequencing, assembly and annotation of the F. buski mt genome. The complete mt genome sequences of the intestinal fluke comprise 14,118 bp and is thus the shortest

  3. Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence

    PubMed Central

    2012-01-01

    Background Along with the draft sequencing of the pig genome, which has been completed by an international consortium, collection of the nucleotide sequences of genes expressed in various tissues and determination of entire cDNA sequences are necessary for investigations of gene function. The sequences of expressed genes are also useful for genome annotation, which is important for isolating the genes responsible for particular traits. Results We performed a large-scale expressed sequence tag (EST) analysis in pigs by using 32 full-length-enriched cDNA libraries derived from 28 kinds of tissues and cells, including seven tissues (brain, cerebellum, colon, hypothalamus, inguinal lymph node, ovary, and spleen) derived from pigs that were cloned from a sow subjected to genome sequencing. We obtained more than 330,000 EST reads from the 5′-ends of the cDNA clones. Comparison with human and bovine gene catalogs revealed that the ESTs corresponded to at least 15,000 genes. cDNA clones representing contigs and singlets generated by assembly of the EST reads were subjected to full-length determination of inserts. We have finished sequencing 31,079 cDNA clones corresponding to more than 12,000 genes. Mapping of the sequences of these cDNA clones on the draft sequence of the pig genome has indicated that the clones are derived from about 15,000 independent loci on the pig genome. Conclusions ESTs and cDNA sequences derived from full-length-enriched libraries are valuable for annotation of the draft sequence of the pig genome. This information will also contribute to the exploration of promoter sequences on the genome and to molecular biology-based analyses in pigs. PMID:23150988

  4. The Ensembl gene annotation system.

    PubMed

    Aken, Bronwen L; Ayling, Sarah; Barrell, Daniel; Clarke, Laura; Curwen, Valery; Fairley, Susan; Fernandez Banet, Julio; Billis, Konstantinos; García Girón, Carlos; Hourlier, Thibaut; Howe, Kevin; Kähäri, Andreas; Kokocinski, Felix; Martin, Fergal J; Murphy, Daniel N; Nag, Rishi; Ruffier, Magali; Schuster, Michael; Tang, Y Amy; Vogel, Jan-Hinnerk; White, Simon; Zadissa, Amonida; Flicek, Paul; Searle, Stephen M J

    2016-01-01

    The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html. PMID:27337980

  5. The Ensembl gene annotation system

    PubMed Central

    Aken, Bronwen L.; Ayling, Sarah; Barrell, Daniel; Clarke, Laura; Curwen, Valery; Fairley, Susan; Fernandez Banet, Julio; Billis, Konstantinos; García Girón, Carlos; Hourlier, Thibaut; Howe, Kevin; Kähäri, Andreas; Kokocinski, Felix; Martin, Fergal J.; Murphy, Daniel N.; Nag, Rishi; Ruffier, Magali; Schuster, Michael; Tang, Y. Amy; Vogel, Jan-Hinnerk; White, Simon; Zadissa, Amonida; Flicek, Paul

    2016-01-01

    The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail. Database URL: http://www.ensembl.org/index.html PMID:27337980

  6. The Vigna Genome Server, 'VigGS': A Genomic Knowledge Base of the Genus Vigna Based on High-Quality, Annotated Genome Sequence of the Azuki Bean, Vigna angularis (Willd.) Ohwi & Ohashi.

    PubMed

    Sakai, Hiroaki; Naito, Ken; Takahashi, Yu; Sato, Toshiyuki; Yamamoto, Toshiya; Muto, Isamu; Itoh, Takeshi; Tomooka, Norihiko

    2016-01-01

    The genus Vigna includes legume crops such as cowpea, mungbean and azuki bean, as well as >100 wild species. A number of the wild species are highly tolerant to severe environmental conditions including high-salinity, acid or alkaline soil; drought; flooding; and pests and diseases. These features of the genus Vigna make it a good target for investigation of genetic diversity in adaptation to stressful environments; however, a lack of genomic information has hindered such research in this genus. Here, we present a genome database of the genus Vigna, Vigna Genome Server ('VigGS', http://viggs.dna.affrc.go.jp), based on the recently sequenced azuki bean genome, which incorporates annotated exon-intron structures, along with evidence for transcripts and proteins, visualized in GBrowse. VigGS also facilitates user construction of multiple alignments between azuki bean genes and those of six related dicot species. In addition, the database displays sequence polymorphisms between azuki bean and its wild relatives and enables users to design primer sequences targeting any variant site. VigGS offers a simple keyword search in addition to sequence similarity searches using BLAST and BLAT. To incorporate up to date genomic information, VigGS automatically receives newly deposited mRNA sequences of pre-set species from the public database once a week. Users can refer to not only gene structures mapped on the azuki bean genome on GBrowse but also relevant literature of the genes. VigGS will contribute to genomic research into plant biotic and abiotic stresses and to the future development of new stress-tolerant crops. PMID:26644460

  7. Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions.

    PubMed

    Deutschbauer, Adam; Price, Morgan N; Wetmore, Kelly M; Shao, Wenjun; Baumohl, Jason K; Xu, Zhuchen; Nguyen, Michelle; Tamse, Raquel; Davis, Ronald W; Arkin, Adam P

    2011-11-01

    Most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function. Given the great diversity of bacteria and the ease of genome sequencing, high-throughput approaches to identify gene function experimentally are needed. Here, we use pools of tagged transposon mutants in the metal-reducing bacterium Shewanella oneidensis MR-1 to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth substrates, alternative electron acceptors, stresses, and motility. We find that 2,350 genes have a pattern of fitness that is significantly different from random and 1,230 of these genes (37% of our total assayed genes) have enough signal to show strong biological correlations. We find that genes in all functional categories have phenotypes, including hundreds of hypotheticals, and that potentially redundant genes (over 50% amino acid identity to another gene in the genome) are also likely to have distinct phenotypes. Using fitness patterns, we were able to propose specific molecular functions for 40 genes or operons that lacked specific annotations or had incomplete annotations. In one example, we demonstrate that the previously hypothetical gene SO_3749 encodes a functional acetylornithine deacetylase, thus filling a missing step in S. oneidensis metabolism. Additionally, we demonstrate that the orphan histidine kinase SO_2742 and orphan response regulator SO_2648 form a signal transduction pathway that activates expression of acetyl-CoA synthase and is required for S. oneidensis to grow on acetate as a carbon source. Lastly, we demonstrate that gene expression and mutant fitness are poorly correlated and that mutant fitness generates more confident predictions of gene function than does gene expression. The approach described here can be applied generally to create large-scale gene-phenotype maps for evidence-based annotation of gene function in prokaryotes. PMID:22125499

  8. Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

    PubMed Central

    Deutschbauer, Adam; Price, Morgan N.; Wetmore, Kelly M.; Shao, Wenjun; Baumohl, Jason K.; Xu, Zhuchen; Nguyen, Michelle; Tamse, Raquel; Davis, Ronald W.; Arkin, Adam P.

    2011-01-01

    Most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function. Given the great diversity of bacteria and the ease of genome sequencing, high-throughput approaches to identify gene function experimentally are needed. Here, we use pools of tagged transposon mutants in the metal-reducing bacterium Shewanella oneidensis MR-1 to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth substrates, alternative electron acceptors, stresses, and motility. We find that 2,350 genes have a pattern of fitness that is significantly different from random and 1,230 of these genes (37% of our total assayed genes) have enough signal to show strong biological correlations. We find that genes in all functional categories have phenotypes, including hundreds of hypotheticals, and that potentially redundant genes (over 50% amino acid identity to another gene in the genome) are also likely to have distinct phenotypes. Using fitness patterns, we were able to propose specific molecular functions for 40 genes or operons that lacked specific annotations or had incomplete annotations. In one example, we demonstrate that the previously hypothetical gene SO_3749 encodes a functional acetylornithine deacetylase, thus filling a missing step in S. oneidensis metabolism. Additionally, we demonstrate that the orphan histidine kinase SO_2742 and orphan response regulator SO_2648 form a signal transduction pathway that activates expression of acetyl-CoA synthase and is required for S. oneidensis to grow on acetate as a carbon source. Lastly, we demonstrate that gene expression and mutant fitness are poorly correlated and that mutant fitness generates more confident predictions of gene function than does gene expression. The approach described here can be applied generally to create large-scale gene-phenotype maps for evidence-based annotation of gene function in prokaryotes. PMID:22125499

  9. Vcfanno: fast, flexible annotation of genetic variants.

    PubMed

    Pedersen, Brent S; Layer, Ryan M; Quinlan, Aaron R

    2016-01-01

    The integration of genome annotations is critical to the identification of genetic variants that are relevant to studies of disease or other traits. However, comprehensive variant annotation with diverse file formats is difficult with existing methods. Here we describe vcfanno, which flexibly extracts and summarizes attributes from multiple annotation files and integrates the annotations within the INFO column of the original VCF file. By leveraging a parallel "chromosome sweeping" algorithm, we demonstrate substantial performance gains by annotating ~85,000 variants per second with 50 attributes from 17 commonly used genome annotation resources. Vcfanno is available at https://github.com/brentp/vcfanno under the MIT license. PMID:27250555

  10. Genomic research, publics and experts in Latin America: Nation, race and body

    PubMed Central

    Wade, Peter; López-Beltrán, Carlos; Restrepo, Eduardo; Santos, Ricardo Ventura

    2015-01-01

    The articles in this issue highlight contributions that studies of Latin America can make to wider debates about the effects of genomic science on public ideas about race and nation. We argue that current ideas about the power of genomics to transfigure and transform existing ways of thinking about human diversity are often overstated. If a range of social contexts are examined, the effects are uneven. Our data show that genomic knowledge can unsettle and reinforce ideas of nation and race; it can be both banal and highly politicized. In this introduction, we outline concepts of genetic knowledge in society; theories of genetics, nation and race; approaches to public understandings of science; and the Latin American contexts of transnational ideas of nation and race. PMID:27479996

  11. Genomic research, publics and experts in Latin America: Nation, race and body.

    PubMed

    Wade, Peter; López-Beltrán, Carlos; Restrepo, Eduardo; Santos, Ricardo Ventura

    2015-12-01

    The articles in this issue highlight contributions that studies of Latin America can make to wider debates about the effects of genomic science on public ideas about race and nation. We argue that current ideas about the power of genomics to transfigure and transform existing ways of thinking about human diversity are often overstated. If a range of social contexts are examined, the effects are uneven. Our data show that genomic knowledge can unsettle and reinforce ideas of nation and race; it can be both banal and highly politicized. In this introduction, we outline concepts of genetic knowledge in society; theories of genetics, nation and race; approaches to public understandings of science; and the Latin American contexts of transnational ideas of nation and race. PMID:27479996

  12. IMG 4 version of the integrated microbial genomes comparative analysis system.

    PubMed

    Markowitz, Victor M; Chen, I-Min A; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Woyke, Tanja; Huntemann, Marcel; Anderson, Iain; Billis, Konstantinos; Varghese, Neha; Mavromatis, Konstantinos; Pati, Amrita; Ivanova, Natalia N; Kyrpides, Nikos C

    2014-01-01

    The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG's data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG's annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu). PMID:24165883

  13. IMG 4 version of the integrated microbial genomes comparative analysis system

    SciTech Connect

    Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Woyke, Tanja; Huntemann, Marcel; Anderson, Iain; Billis, Konstantinos; Varghese, Neha; Mavromatis, Konstantinos; Pati, Amrita; Ivanova, Natalia N.; Kyrpides, Nikos C.

    2013-10-27

    The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Finally, different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).

  14. Functional Annotation of the Ophiostoma novo-ulmi Genome: Insights into the Phytopathogenicity of the Fungal Agent of Dutch Elm Disease

    PubMed Central

    Comeau, André M.; Dufour, Josée; Bouvet, Guillaume F.; Jacobi, Volker; Nigg, Martha; Henrissat, Bernard; Laroche, Jérôme; Levesque, Roger C.; Bernier, Louis

    2015-01-01

    The ascomycete fungus Ophiostoma novo-ulmi is responsible for the pandemic of Dutch elm disease that has been ravaging Europe and North America for 50 years. We proceeded to annotate the genome of the O. novo-ulmi strain H327 that was sequenced in 2012. The 31.784-Mb nuclear genome (50.1% GC) is organized into 8 chromosomes containing a total of 8,640 protein-coding genes that we validated with RNA sequencing analysis. Approximately 53% of these genes have their closest match to Grosmannia clavigera kw1407, followed by 36% in other close Sordariomycetes, 5% in other Pezizomycotina, and surprisingly few (5%) orphans. A relatively small portion (∼3.4%) of the genome is occupied by repeat sequences; however, the mechanism of repeat-induced point mutation appears active in this genome. Approximately 76% of the proteins could be assigned functions using Gene Ontology analysis; we identified 311 carbohydrate-active enzymes, 48 cytochrome P450s, and 1,731 proteins potentially involved in pathogen–host interaction, along with 7 clusters of fungal secondary metabolites. Complementary mating-type locus sequencing, mating tests, and culturing in the presence of elm terpenes were conducted. Our analysis identified a specific genetic arsenal impacting the sexual and vegetative growth, phytopathogenicity, and signaling/plant–defense–degradation relationship between O. novo-ulmi and its elm host and insect vectors. PMID:25539722

  15. Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales

    PubMed Central

    Cristancho, Marco A.; Botero-Rozo, David Octavio; Giraldo, William; Tabima, Javier; Riaño-Pachón, Diego Mauricio; Escobar, Carolina; Rozo, Yomara; Rivera, Luis F.; Durán, Andrés; Restrepo, Silvia; Eilam, Tamar; Anikster, Yehoshua; Gaitán, Alvaro L.

    2014-01-01

    Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates. PMID

  16. Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults

    PubMed Central

    Close, James; Game, Laurence; Clark, Barnaby; Bergounioux, Jean; Gerovassili, Ageliki; Thein, Swee Lay

    2004-01-01

    Background Heterocellular hereditary persistence of fetal hemoglobin (HPFH) is a common multifactorial trait characterized by a modest increase of fetal hemoglobin levels in adults. We previously localized a Quantitative Trait Locus for HPFH in an extensive Asian-Indian kindred to chromosome 6q23. As part of the strategy of positional cloning and a means towards identification of the specific genetic alteration in this family, a thorough annotation of the candidate interval based on a strategy of in silico / wet biology approach with comparative genomics was conducted. Results The ~1.5 Mb candidate region was shown to contain five protein-coding genes. We discovered a very large uncharacterized gene containing WD40 and SH3 domains (AHI1), and extended the annotation of four previously characterized genes (MYB, ALDH8A1, HBS1L and PDE7B). We also identified several genes that do not appear to be protein coding, and generated 17 kb of novel transcript sequence data from re-sequencing 97 EST clones. Conclusion Detailed and thorough annotation of this 1.5 Mb interval in 6q confirms a high level of aberrant transcripts in testicular tissue. The candidate interval was shown to exhibit an extraordinary level of alternate splicing – 19 transcripts were identified for the 5 protein coding genes, but it appears that a significant portion (14/19) of these alternate transcripts did not have an open reading frame, hence their functional role is questionable. These transcripts may result from aberrant rather than regulated splicing. PMID:15169551

  17. All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs.

    PubMed

    Schork, Andrew J; Thompson, Wesley K; Pham, Phillip; Torkamani, Ali; Roddey, J Cooper; Sullivan, Patrick F; Kelsoe, John R; O'Donovan, Michael C; Furberg, Helena; Schork, Nicholas J; Andreassen, Ole A; Dale, Anders M

    2013-04-01

    Recent results indicate that genome-wide association studies (GWAS) have the potential to explain much of the heritability of common complex phenotypes, but methods are lacking to reliably identify the remaining associated single nucleotide polymorphisms (SNPs). We applied stratified False Discovery Rate (sFDR) methods to leverage genic enrichment in GWAS summary statistics data to uncover new loci likely to replicate in independent samples. Specifically, we use linkage disequilibrium-weighted annotations for each SNP in combination with nominal p-values to estimate the True Discovery Rate (TDR = 1-FDR) for strata determined by different genic categories. We show a consistent pattern of enrichment of polygenic effects in specific annotation categories across diverse phenotypes, with the greatest enrichment for SNPs tagging regulatory and coding genic elements, little enrichment in introns, and negative enrichment for intergenic SNPs. Stratified enrichment directly leads to increased TDR for a given p-value, mirrored by increased replication rates in independent samples. We show this in independent Crohn's disease GWAS, where we find a hundredfold variation in replication rate across genic categories. Applying a well-established sFDR methodology we demonstrate the utility of stratification for improving power of GWAS in complex phenotypes, with increased rejection rates from 20% in height to 300% in schizophrenia with traditional FDR and sFDR both fixed at 0.05. Our analyses demonstrate an inherent stratification among GWAS SNPs with important conceptual implications that can be leveraged by statistical methods to improve the discovery of loci. PMID:23637621

  18. Genome Annotation by Shotgun Inactivation of a Native Gene in Hemizygous Cells: Application to BRCA2 with Implication of Hypomorphic Variants

    PubMed Central

    Ghosh, Soma; Bhunia, Anil K.; Paun, Bogdan C.; Gilbert, Samuel F.; Dhru, Urmil; Patel, Kalpesh; Kern, Scott E.

    2015-01-01

    The greatest interpretive challenge of modern medicine may be to functionally annotate the vast variation of human genomes. Demonstrating a proposed approach, we created a library of BRCA2 exon 27 shotgun-mutant plasmids including solitary and multiplex mutations to generate human knockin clones using homologous recombination. This 55-mutation, 13-clone syngeneic variance library (SyVaL) comprised severely affected clones having early-stop nonsense mutations, functionally hypomorphic clones having multiple missense mutations emphasizing the potential to identify and assess hypomorphic mutations in novel proteomic and epidemiologic studies, and neutral clones having multiple missense mutations. Efficient coverage of nonessential amino acids was provided by mutation multiplexing. Severe mutations were distinguished from hypomorphic or neutral changes by chemosensitivity assays (hypersensitivity to mitomycin C and acetaldehyde), by analysis of RAD51 focus formation, and by mitotic multipolarity. A multiplex unbiased approach of generating all-human SyVaLs in medically important genes, with random mutations in native genes, would provide databases of variants that could be functionally annotated without concerns arising from exogenous cDNA constructs or interspecies interactions, as a basis for subsequent proteomic domain mapping or clinical calibration if desired. Such gene-irrelevant approaches could be scaled up for multiple genes of clinical interest, providing distributable cellular libraries linked to public-shared functional databases. PMID:25451944

  19. Assembly and annotation of full mitochondrial genomes for the corn rootworm species, Diabrotica virgifera virgifera and Diabrotica barberi (Insecta: Coleoptera: Chrysomelidae), using Next Generation Sequence data.

    PubMed

    Coates, Brad S

    2014-06-01

    Complete mitochondrial genomes for two corn rootworm species, Diabrotica virgifera virgifera (16,747 bp) and Diabrotica barberi (16,632; Insecta: Coleoptera: Chrysomelidae), were assembled from Illumina HiSeq2000 read data. Annotation indicated that the order and orientation of 13 protein coding genes (PCGs), and 22 tRNA and 2 rRNA sequences were in typical of insect mitochondrial genomes. Non-standard nad4 and cox3 stop codons were composed of single T nucleotides and likely completed by adenylation, and atypical TTT start codons was predicted for both D. v. virgifera and D. barberinad1 genes. The D. v. virgifera and D. barberi haplotypes showed 819 variable nucleotide positions within PCG regions (7.36% divergence), which suggest that speciation may have occurred ~3.68 million years ago assuming a linear rate of short-term substitution. Phylogenetic analyses of Coleopteran MtD genome show clustering based on family level, and may have the capacity to resolve the evolutionary history within this Order of insects. PMID:24657060

  20. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that i...

  1. Intraspecific comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The mitochondrial genomes of two isolates of the wheat pathogen Mycosphaerella graminicola were sequenced completely and compared to identify polymorphic regions. This organism is of interest because it is phylogenetically distant from other fungi with sequenced mitochondrial genomes and it has show...

  2. Expert reports.

    PubMed

    Thornton, R G

    2000-10-01

    In 1996, article 4590i of the Texas Revised Civil Statutes Annotated, the statutory provision that governs health care liability claims in Texas, was amended to require claimants to file expert reports within 180 days as part of the prosecution of their claims. Sufficient expert reports include explanations of the standard of care, the deviation from that standard, and how the deviation caused the claimant's damages. Two provisions allow courts to grant a 30-day extension for filing expert reports. A good cause extension can be used to extend the filing deadline to 210 days; however, case law has not clearly defined what constitutes good cause. An accident or mistake grace period can be used to justify reports filed >210 days after the suit has been filed; judges determine whether the failure is due to a mistake or intentional indifference. As with any statute, the language is not as important as how the courts (judges) interpret that language. The statute may appear strict but room for interpretation exists. PMID:16389359

  3. Algal functional annotation tool

    SciTech Connect

    Lopez, D.; Casero, D.; Cokus, S. J.; Merchant, S. S.; Pellegrini, M.

    2012-07-01

    The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on KEGG pathway maps and batch gene identifier conversion.

  4. Whole-Genome Sequencing and Annotation of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum annuum (Bird's Eye Chili) and Capsicum chinense (Yellow Lantern Chili), Respectively.

    PubMed

    Gan, Huan You; Gan, Han Ming; Savka, Michael A; Triassi, Alexander J; Wheatley, Matthew S; Naqvi, Kubra F; Foxhall, Taylor E; Anauo, Michael J; Baldwin, Mariah L; Burkhardt, Russell N; O'Bryon, Isabelle G; Dailey, Lucas K; Busairi, Nurfatini Idayu; Keith, Robert C; Khair, Megat Hazmah Megat Mazhar; Rasul, Muhammad Zamir Mohd; Rosdi, Nur Aiman Mohd; Mountzouros, James R; Rhoads, Aleigha C; Selochan, Melissa A; Tautanov, Timur B; Polter, Steven J; Marks, Kayla D; Caraballo, Alexander A; Hudson, André O

    2015-01-01

    Here, we report the genome sequences of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum spp. Annotation revealed gene clusters for the synthesis of bacilysin, lichensin, and bacillibactin and sporulation killing factor (skfA) in Bacillus safensis RIT372 and turnerbactin and carotenoid in Pseudomonas oryzihabitans RIT370. PMID:25883290

  5. Whole-Genome Sequencing and Annotation of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum annuum (Bird’s Eye Chili) and Capsicum chinense (Yellow Lantern Chili), Respectively

    PubMed Central

    Gan, Huan You; Gan, Han Ming; Savka, Michael A.; Triassi, Alexander J.; Wheatley, Matthew S.; Naqvi, Kubra F.; Foxhall, Taylor E.; Anauo, Michael J.; Baldwin, Mariah L.; Burkhardt, Russell N.; O’Bryon, Isabelle G.; Dailey, Lucas K.; Busairi, Nurfatini Idayu; Keith, Robert C.; Khair, Megat Hazmah Megat Mazhar; Rasul, Muhammad Zamir Mohd; Rosdi, Nur Aiman Mohd; Mountzouros, James R.; Rhoads, Aleigha C.; Selochan, Melissa A.; Tautanov, Timur B.; Polter, Steven J.; Marks, Kayla D.; Caraballo, Alexander A.

    2015-01-01

    Here, we report the genome sequences of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum spp. Annotation revealed gene clusters for the synthesis of bacilysin, lichensin, and bacillibactin and sporulation killing factor (skfA) in Bacillus safensis RIT372 and turnerbactin and carotenoid in Pseudomonas oryzihabitans RIT370. PMID:25883290

  6. Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features

    PubMed Central

    Cui, Xiaodong; Wei, Zhen; Zhang, Lin; Liu, Hui; Sun, Lei; Zhang, Shao-Wu; Huang, Yufei; Meng, Jia

    2016-01-01

    Biological features, such as genes and transcription factor binding sites, are often denoted with genome-based coordinates as the genomic features. While genome-based representation is usually very effective in correlating various biological features, it can be tedious to examine the relationship between RNA-related genomic features and the landmarks of RNA transcripts with existing tools due to the difficulty in the conversion between genome-based coordinates and RNA-based coordinates. We developed here an open source Guitar R/Bioconductor package for sketching the transcriptomic view of RNA-related biological features represented by genome based coordinates. Internally, Guitar package extracts the standardized RNA coordinates with respect to the landmarks of RNA transcripts, with which hundreds of millions of RNA-related genomic features can then be efficiently analyzed within minutes. We demonstrated the usage of Guitar package in analyzing posttranscriptional RNA modifications (5-methylcytosine and N6-methyladenosine) derived from high-throughput sequencing approaches (MeRIP-Seq and RNA BS-Seq) and show that RNA 5-methylcytosine (m5C) is enriched in 5′UTR. The newly developed Guitar R/Bioconductor package achieves stable performance on the data tested and revealed novel biological insights. It will effectively facilitate the analysis of RNA methylation data and other RNA-related biological features in the future. PMID:27239475

  7. Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features.

    PubMed

    Cui, Xiaodong; Wei, Zhen; Zhang, Lin; Liu, Hui; Sun, Lei; Zhang, Shao-Wu; Huang, Yufei; Meng, Jia

    2016-01-01

    Biological features, such as genes and transcription factor binding sites, are often denoted with genome-based coordinates as the genomic features. While genome-based representation is usually very effective in correlating various biological features, it can be tedious to examine the relationship between RNA-related genomic features and the landmarks of RNA transcripts with existing tools due to the difficulty in the conversion between genome-based coordinates and RNA-based coordinates. We developed here an open source Guitar R/Bioconductor package for sketching the transcriptomic view of RNA-related biological features represented by genome based coordinates. Internally, Guitar package extracts the standardized RNA coordinates with respect to the landmarks of RNA transcripts, with which hundreds of millions of RNA-related genomic features can then be efficiently analyzed within minutes. We demonstrated the usage of Guitar package in analyzing posttranscriptional RNA modifications (5-methylcytosine and N6-methyladenosine) derived from high-throughput sequencing approaches (MeRIP-Seq and RNA BS-Seq) and show that RNA 5-methylcytosine (m(5)C) is enriched in 5'UTR. The newly developed Guitar R/Bioconductor package achieves stable performance on the data tested and revealed novel biological insights. It will effectively facilitate the analysis of RNA methylation data and other RNA-related biological features in the future. PMID:27239475

  8. De Novo Assembly and Annotation of the Asian Tiger Mosquito (Aedes albopictus) Repeatome with dnaPipeTE from Raw Genomic Reads and Comparative Analysis with the Yellow Fever Mosquito (Aedes aegypti)

    PubMed Central

    Goubert, Clément; Modolo, Laurent; Vieira, Cristina; ValienteMoro, Claire; Mavingui, Patrick; Boulesteix, Matthieu

    2015-01-01

    Repetitive DNA, including transposable elements (TEs), is found throughout eukaryotic genomes. Annotating and assembling the “repeatome” during genome-wide analysis often poses a challenge. To address this problem, we present dnaPipeTE—a new bioinformatics pipeline that uses a sample of raw genomic reads. It produces precise estimates of repeated DNA content and TE consensus sequences, as well as the relative ages of TE families. We shows that dnaPipeTE performs well using very low coverage sequencing in different genomes, losing accuracy only with old TE families. We applied this pipeline to the genome of the Asian tiger mosquito Aedes albopictus, an invasive species of human health interest, for which the genome size is estimated to be over 1 Gbp. Using dnaPipeTE, we showed that this species harbors a large (50% of the genome) and potentially active repeatome with an overall TE class and order composition similar to that of Aedes aegypti, the yellow fever mosquito. However, intraorder dynamics show clear distinctions between the two species, with differences at the TE family level. Our pipeline’s ability to manage the repeatome annotation problem will make it helpful for new or ongoing assembly projects, and our results will benefit future genomic studies of A. albopictus. PMID:25767248

  9. Genome annotation provides insight into carbon monoxide and hydrogen metabolism in Rubrivivax gelatinosus

    SciTech Connect

    Wawrousek, Karen; Noble, Scott; Korlach, Jonas; Eckert, Carrie; Yu, Jianping; Maness, Pin -Ching

    2014-12-05

    In this article, we report here the sequencing and analysis of the genome of the purple non-sulfur photosynthetic bacterium Rubrivivax gelatinosus CBS. This microbe is a model for studies of its carboxydotrophic life style under anaerobic condition, based on its ability to utilize carbon monoxide (CO) as the sole carbon substrate and water as the electron acceptor, yielding CO2 and H2 as the end products. The CO-oxidation reaction is known to be catalyzed by two enzyme complexes, the CO dehydrogenase and hydrogenase. As expected, analysis of the genome of Rx. gelatinosus CBS reveals the presence of genes encoding both enzyme complexes. The CO-oxidation reaction is CO-inducible, which is consistent with the presence of two putative CO-sensing transcription factors in its genome. Genome analysis also reveals the presence of two additional hydrogenases, an uptake hydrogenase that liberates the electrons in H2 in support of cell growth, and a regulatory hydrogenase that senses H2 and relays the signal to a two-component system that ultimately controls synthesis of the uptake hydrogenase. The genome also contains two sets of hydrogenase maturation genes which are known to assemble the catalytic metallocluster of the hydrogenase NiFe active site. Finally and collectively, the genome sequence and analysis information reveals the blueprint of an intricate network of signal transduction pathways and its underlying regulation that enables Rx. gelatinosus CBS to thrive on CO or H2 in support of cell growth.

  10. Interspecific Comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola

    SciTech Connect

    Millenbaugh, Bonnie A; Pangilinan, Jasmyn L.; Torriani, Stefano F.F.; Goodwin, Stephen B.; Kema, Gert H.J.; McDonald, Bruce A.

    2007-12-07

    The mitochondrial genomes of two isolates of the wheat pathogen Mycosphaerella graminicola were sequenced completely and compared to identify polymorphic regions. This organism is of interest because it is phylogenetically distant from other fungi with sequenced mitochondrial genomes and it has shown discordant patterns of nuclear and mitochondrial diversity. The mitochondrial genome of M. graminicola is a circular molecule of approximately 43,960 bp containing the typical genes coding for 14 proteins related to oxidative phosphorylation, one RNA polymerase, two rRNA genes and a set of 27 tRNAs. The mitochondrial DNA of M. graminicola lacks the gene encoding the putative ribosomal protein (rps5-like), commonly found in fungal mitochondrial genomes. Most of the tRNA genes were clustered with a gene order conserved with many other ascomycetes. A sample of thirty-five additional strains representing the known global mt diversity was partially sequenced to measure overall mitochondrial variability within the species. Little variation was found, confirming previous RFLP-based findings of low mitochondrial diversity. The mitochondrial sequence of M. graminicola is the first reported from the family Mycosphaerellaceae or the order Capnodiales. The sequence also provides a tool to better understand the development of fungicide resistance and the conflicting pattern of high nuclear and low mitochondrial diversity in global populations of this fungus.

  11. Intraspecific comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complete mitochondrial genome of the plant pathogenic fungus Mycosphaerella graminicola is a circular molecule of 43,961 bp containing the typical genes coding for 14 proteins related to oxidative phosphorylation, one RNA polymerase, two rRNA genes and a set of 27 tRNAs. Most of the tRNA genes w...

  12. Annotation of the Modular Polyketide Synthase and Nonribosomal Peptide Synthetase Gene Clusters in the Genome of Streptomyces tsukubaensis NRRL18488

    PubMed Central

    Blažič, Marko; Starcevic, Antonio; Lisfi, Mohamed; Baranasic, Damir; Goranovič, Dušan; Fujs, Štefan; Kuščer, Enej; Kosec, Gregor; Petković, Hrvoje; Cullum, John; Hranueli, Daslav

    2012-01-01

    The high G+C content and large genome size make the sequencing and assembly of Streptomyces genomes more difficult than for other bacteria. Many pharmaceutically important natural products are synthesized by modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The analysis of such gene clusters is difficult if the genome sequence is not of the highest quality, because clusters can be distributed over several contigs, and sequencing errors can introduce apparent frameshifts into the large PKS and NRPS proteins. An additional problem is that the modular nature of the clusters results in the presence of imperfect repeats, which may cause assembly errors. The genome sequence of Streptomyces tsukubaensis NRRL18488 was scanned for potential PKS and NRPS modular clusters. A phylogenetic approach was used to identify multiple contigs belonging to the same cluster. Four PKS clusters and six NRPS clusters were identified. Contigs containing cluster sequences were analyzed in detail by using the ClustScan program, which suggested the order and orientation of the contigs. The sequencing of the appropriate PCR products confirmed the ordering and allowed the correction of apparent frameshifts resulting from sequencing errors. The product chemistry of such correctly assembled clusters could also be predicted. The analysis of one PKS cluster showed that it should produce a bafilomycin-like compound, and reverse transcription (RT)-PCR was used to show that the cluster was transcribed. PMID:22983969

  13. Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As life scientists continue to pursue various ‘omics-based research, there is a need make available, high quality data for the most fundamental ‘omics of all: genomics. The bacterium Paenibacillus larvae is the causative agent of the honey bee disease American Foulbrood. If untreated, it can lead to...

  14. Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity.

    PubMed

    Philippe, Nicolas; Boureux, Anthony; Bréhélin, Laurent; Tarhio, Jorma; Commes, Thérèse; Rivals, Eric

    2009-08-01

    Ultra high-throughput sequencing is used to analyse the transcriptome or interactome at unprecedented depth on a genome-wide scale. These techniques yield short sequence reads that are then mapped on a genome sequence to predict putatively transcribed or protein-interacting regions. We argue that factors such as background distribution, sequence errors, and read length impact on the prediction capacity of sequence census experiments. Here we suggest a computational approach to measure these factors and analyse their influence on both transcriptomic and epigenomic assays. This investigation provides new clues on both methodological and biological issues. For instance, by analysing chromatin immunoprecipitation read sets, we estimate that 4.6% of reads are affected by SNPs. We show that, although the nucleotide error probability is low, it significantly increases with the position in the sequence. Choosing a read length above 19 bp practically eliminates the risk of finding irrelevant positions, while above 20 bp the number of uniquely mapped reads decreases. With our procedure, we obtain 0.6% false positives among genomic locations. Hence, even rare signatures should identify biologically relevant regions, if they are mapped on the genome. This indicates that digital transcriptomics may help to characterize the wealth of yet undiscovered, low-abundance transcripts. PMID:19531739

  15. An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background A comprehensive transcriptome survey, or gene atlas, provides information essential for a complete understanding of the genomic biology of an organism. We present an atlas of RNA abundance for 92 adult, juvenile and fetal cattle tissues and three cattle cell lines. Results The Bovine Gene...

  16. Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity

    PubMed Central

    Philippe, Nicolas; Boureux, Anthony; Bréhélin, Laurent; Tarhio, Jorma; Commes, Thérèse; Rivals, Éric

    2009-01-01

    Ultra high-throughput sequencing is used to analyse the transcriptome or interactome at unprecedented depth on a genome-wide scale. These techniques yield short sequence reads that are then mapped on a genome sequence to predict putatively transcribed or protein-interacting regions. We argue that factors such as background distribution, sequence errors, and read length impact on the prediction capacity of sequence census experiments. Here we suggest a computational approach to measure these factors and analyse their influence on both transcriptomic and epigenomic assays. This investigation provides new clues on both methodological and biological issues. For instance, by analysing chromatin immunoprecipitation read sets, we estimate that 4.6% of reads are affected by SNPs. We show that, although the nucleotide error probability is low, it significantly increases with the position in the sequence. Choosing a read length above 19 bp practically eliminates the risk of finding irrelevant positions, while above 20 bp the number of uniquely mapped reads decreases. With our procedure, we obtain 0.6% false positives among genomic locations. Hence, even rare signatures should identify biologically relevant regions, if they are mapped on the genome. This indicates that digital transcriptomics may help to characterize the wealth of yet undiscovered, low-abundance transcripts. PMID:19531739

  17. Gene Ontology annotations and resources.

    PubMed

    Blake, J A; Dolan, M; Drabkin, H; Hill, D P; Li, Ni; Sitnikov, D; Bridges, S; Burgess, S; Buza, T; McCarthy, F; Peddinti, D; Pillai, L; Carbon, S; Dietze, H; Ireland, A; Lewis, S E; Mungall, C J; Gaudet, P; Chrisholm, R L; Fey, P; Kibbe, W A; Basu, S; Siegele, D A; McIntosh, B K; Renfro, D P; Zweifel, A E; Hu, J C; Brown, N H; Tweedie, S; Alam-Faruque, Y; Apweiler, R; Auchinchloss, A; Axelsen, K; Bely, B; Blatter, M -C; Bonilla, C; Bouguerleret, L; Boutet, E; Breuza, L; Bridge, A; Chan, W M; Chavali, G; Coudert, E; Dimmer, E; Estreicher, A; Famiglietti, L; Feuermann, M; Gos, A; Gruaz-Gumowski, N; Hieta, R; Hinz, C; Hulo, C; Huntley, R; James, J; Jungo, F; Keller, G; Laiho, K; Legge, D; Lemercier, P; Lieberherr, D; Magrane, M; Martin, M J; Masson, P; Mutowo-Muellenet, P; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Porras Millán, P; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Stutz, A; Sundaram, S; Tognolli, M; Xenarios, I; Foulgar, R; Lomax, J; Roncaglia, P; Khodiyar, V K; Lovering, R C; Talmud, P J; Chibucos, M; Giglio, M Gwinn; Chang, H -Y; Hunter, S; McAnulla, C; Mitchell, A; Sangrador, A; Stephan, R; Harris, M A; Oliver, S G; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, P J; McDowall, D M; Staines, D M; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, T; Wang, S -J; Petri, V; Lowry, T; D'Eustachio, P; Matthews, L; Balakrishnan, R; Binkley, G; Cherry, J M; Costanzo, M C; Dwight, S S; Engel, S R; Fisk, D G; Hitz, B C; Hong, E L; Karra, K; Miyasato, S R; Nash, R S; Park, J; Skrzypek, M S; Weng, S; Wong, E D; Berardini, T Z; Huala, E; Mi, H; Thomas, P D; Chan, J; Kishore, R; Sternberg, P; Van Auken, K; Howe, D; Westerfield, M

    2013-01-01

    The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources. PMID:23161678

  18. Genomewide annotation and comparative genomics of cytochrome P450 monooxygenases (P450s) in the polypore species Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora.

    PubMed

    Syed, Khajamohiddin; Nelson, David R; Riley, Robert; Yadav, Jagjit S

    2013-01-01

    Genomewide annotation of cytochrome P450 monooxygenases (P450s) in three white-rot species of the fungal order Polyporales, namely Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora, revealed a large contingent of P450 genes (P450ome) in their genomes. A total of 199 P450 genes in B. adusta and 209 P450 genes each in Ganoderma sp. and P. brevispora were identified. These P450omes were classified into families and subfamilies as follows: B. adusta (39 families, 86 subfamilies), Ganoderma sp. (41 families, 105 subfamilies) and P. brevispora (42 families, 111 subfamilies). Of note, the B. adusta genome lacked the CYP505 family (P450foxy), a group of P450-CPR fusion proteins. The three polypore species revealed differential enrichment of individual P450 families in their genomes. The largest CYP families in the three genomes were CYP5144 (67 P450s), CYP5359 (46 P450s) and CYP5344 (43 P450s) in B. adusta, Ganoderma sp. and P. brevispora, respectively. Our analyses showed that tandem gene duplications led to expansions in certain P450 families. An estimated 33% (72 P450s), 28% (55 P450s) and 23% (49 P450s) of P450ome genes were duplicated in P. brevispora, B. adusta and Ganoderma sp., respectively. Family-wise comparative analysis revealed that 22 CYP families are common across the three Polypore species. Comparative P450ome analysis with Ganoderma lucidum revealed the presence of 143 orthologs and 56 paralogs in Ganoderma sp. Multiple P450s were found near the characteristic biosynthetic genes for secondary metabolites, namely polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), terpene cyclase and terpene synthase in the three genomes, suggesting a likely role of these P450s in secondary metabolism in these Polyporales. Overall, the three species had a richer P450 diversity both in terms of the P450 genes and P450 subfamilies as compared to the model white-rot and brown-rot polypore species Phanerochaete chrysosporium and Postia placenta. PMID

  19. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species.

    PubMed

    Wang, Yi; Coleman-Derr, Devin; Chen, Guoping; Gu, Yong Q

    2015-07-01

    Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that is useful for genome wide comparisons and visualization of orthologous clusters. OrthoVenn provides coverage of vertebrates, metazoa, protists, fungi, plants and bacteria for the comparison of orthologous clusters and also supports uploading of customized protein sequences from user-defined species. An interactive Venn diagram, summary counts, and functional summaries of the disjunction and intersection of clusters shared between species are displayed as part of the OrthoVenn result. OrthoVenn also includes in-depth views of the clusters using various sequence analysis tools. Furthermore, OrthoVenn identifies orthologous clusters of single copy genes and allows for a customized search of clusters of specific genes through key words or BLAST. OrthoVenn is an efficient and user-friendly web server freely accessible at http://probes.pw.usda.gov/OrthoVenn or http://aegilops.wheat.ucdavis.edu/OrthoVenn. PMID:25964301

  20. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

    PubMed Central

    Medema, Marnix H.; Blin, Kai; Cimermancic, Peter; de Jager, Victor; Zakrzewski, Piotr; Fischbach, Michael A.; Weber, Tilmann; Takano, Eriko

    2011-01-01

    Bacterial and fungal secondary metabolism is a rich source of novel bioactive compounds with potential pharmaceutical applications as antibiotics, anti-tumor drugs or cholesterol-lowering drugs. To find new drug candidates, microbiologists are increasingly relying on sequencing genomes of a wide variety of microbes. However, rapidly and reliably pinpointing all the potential gene clusters for secondary metabolites in dozens of newly sequenced genomes has been extremely challenging, due to their biochemical heterogeneity, the presence of unknown enzymes and the dispersed nature of the necessary specialized bioinformatics tools and resources. Here, we present antiSMASH (antibiotics & Secondary Metabolite Analysis Shell), the first comprehensive pipeline capable of identifying biosynthetic loci covering the whole range of known secondary metabolite compound classes (polyketides, non-ribosomal peptides, terpenes, aminoglycosides, aminocoumarins, indolocarbazoles, lantibiotics, bacteriocins, nucleosides, beta-lactams, butyrolactones, siderophores, melanins and others). It aligns the identified regions at the gene cluster level to their nearest relatives from a database containing all other known gene clusters, and integrates or cross-links all previously available secondary-metabolite specific gene analysis methods in one interactive view. antiSMASH is available at http://antismash.secondarymetabolites.org. PMID:21672958

  1. Annotation of differentially expressed genes in the somatic embryogenesis of musa and their location in the banana genome.

    PubMed

    Maldonado-Borges, Josefina Ines; Ku-Cauich, José Roberto; Escobedo-Graciamedrano, Rosa Maria

    2013-01-01

    Analysis of cDNA-AFLP was used to study the genes expressed in zygotic and somatic embryogenesis of Musa acuminata Colla ssp. malaccensis, and a comparison was made between their differential transcribed fragments (TDFs) and the sequenced genome of the double haploid- (DH-) Pahang of the malaccensis subspecies that is available in the network. A total of 253 transcript-derived fragments (TDFs) were detected with apparent size of 100-4000 bp using 5 pairs of AFLP primers, of which 21 were differentially expressed during the different stages of banana embryogenesis; 15 of the sequences have matched DH-Pahang chromosomes, with 7 of them being homologous to gene sequences encoding either known or putative protein domains of higher plants. Four TDF sequences were located in all Musa chromosomes, while the rest were located in one or two chromosomes. Their putative individual function is briefly reviewed based on published information, and the potential roles of these genes in embryo development are discussed. Thus the availability of the genome of Musa and the information of TDFs sequences presented here opens new possibilities for an in-depth study of the molecular and biochemical research of zygotic and somatic embryogenesis of Musa. PMID:24027442

  2. Genome-wide prediction and annotation of Burkholderia pseudomallei AraC/XylS family transcription regulator.

    PubMed

    Lim, Boon-San; Chong, Chan-Eng; Zamrod, Zulkeflie; Nathan, Sheila; Mohamed, Rahmah

    2007-01-01

    Many members of the AraC/XylS family transcription regulator have been proven to play a critical role in regulating bacterial virulence factors in response to environmental stress. By using the Hidden Markov Model (HMM) profile built from the alignment of a 99 amino acid conserved domain sequence of 273 AraC/XylS family transcription regulators, we detected a total of 45 AraC/XylS family transcription regulators in the genome of the Gram-negative pathogen, Burkholderia pseudomallei. Further in silico analysis of each detected AraC/XylS family transcription regulatory protein and its neighboring genes allowed us to make a first-order guess on the role of some of these transcription regulators in regulating important virulence factors such as those involved in three type III secretion systems and biosynthesis of pyochelin, exopolysaccharide (EPS) and phospholipase C. This paper has demonstrated an efficient and systematic genome-wide scale prediction of the AraC/XylS family that can be applied to other protein families. PMID:18391231

  3. Annotated ESTs from various tissues of the brown planthopper Nilaparvata lugens: A genomic resource for studying agricultural pests

    PubMed Central

    Noda, Hiroaki; Kawai, Sawako; Koizumi, Yoko; Matsui, Kageaki; Zhang, Qiang; Furukawa, Shigetoyo; Shimomura, Michihiko; Mita, Kazuei

    2008-01-01

    Background The brown planthopper (BPH), Nilaparvata lugens (Hemiptera, Delphacidae), is a serious insect pests of rice plants. Major means of BPH control are application of agricultural chemicals and cultivation of BPH resistant rice varieties. Nevertheless, BPH strains that are resistant to agricultural chemicals have developed, and BPH strains have appeared that are virulent against the resistant rice varieties. Expressed sequence tag (EST) analysis and related applications are useful to elucidate the mechanisms of resistance and virulence and to reveal physiological aspects of this non-model insect, with its poorly understood genetic background. Results More than 37,000 high-quality ESTs, excluding sequences of mitochondrial genome, microbial genomes, and rDNA, have been produced from 18 libraries of various BPH tissues and stages. About 10,200 clusters have been made from whole EST sequences, with average EST size of 627 bp. Among the top ten most abundantly expressed genes, three are unique and show no homology in BLAST searches. The actin gene was highly expressed in BPH, especially in the thorax. Tissue-specifically expressed genes were extracted based on the expression frequency among the libraries. An EST database is available at our web site. Conclusion The EST library will provide useful information for transcriptional analyses, proteomic analyses, and gene functional analyses of BPH. Moreover, specific genes for hemimetabolous insects will be identified. The microarray fabricated based on the EST information will be useful for finding genes related to agricultural and biological problems related to this pest. PMID:18315884

  4. Functional genomics tools applied to plant metabolism: a survey on plant respiration, its connections and the annotation of complex gene functions

    PubMed Central

    Araújo, Wagner L.; Nunes-Nesi, Adriano; Williams, Thomas C. R.

    2012-01-01

    The application of post-genomic techniques in plant respiration studies has greatly improved our ability to assign functions to gene products. In addition it has also revealed previously unappreciated interactions between distal elements of metabolism. Such results have reinforced the need to consider plant respiratory metabolism as part of a complex network and making sense of such interactions will ultimately require the construction of predictive and mechanistic models. Transcriptomics, proteomics, metabolomics, and the quantification of metabolic flux will be of great value in creating such models both by facilitating the annotation of complex gene function, determining their structure and by furnishing the quantitative data required to test them. In this review, we highlight how these experimental approaches have contributed to our current understanding of plant respiratory metabolism and its interplay with associated process (e.g., photosynthesis, photorespiration, and nitrogen metabolism). We also discuss how data from these techniques may be integrated, with the ultimate aim of identifying mechanisms that control and regulate plant respiration and discovering novel gene functions with potential biotechnological implications. PMID:22973288

  5. Rapid High Resolution Genotyping of Francisella tularensis by Whole Genome Sequence Comparison of Annotated Genes (“MLST+”)

    PubMed Central

    Mellmann, Alexander; Höppner, Sebastian; Splettstoesser, Wolf D.; Harmsen, Dag

    2015-01-01

    The zoonotic disease tularemia is caused by the bacterium Francisella tularensis. This pathogen is considered as a category A select agent with potential to be misused in bioterrorism. Molecular typing based on DNA-sequence like canSNP-typing or MLVA has become the accepted standard for this organism. Due to the organism’s highly clonal nature, the current typing methods have reached their limit of discrimination for classifying closely related subpopulations within the subspecies F. tularensis ssp. holarctica. We introduce a new gene-by-gene approach, MLST+, based on whole genome data of 15 sequenced F. tularensis ssp. holarctica strains and apply this approach to investigate an epidemic of lethal tularemia among non-human primates in two animal facilities in Germany. Due to the high resolution of MLST+ we are able to demonstrate that three independent clones of this highly infectious pathogen were responsible for these spatially and temporally restricted outbreaks. PMID:25856198

  6. Gene Ontology Annotations and Resources

    PubMed Central

    2013-01-01

    The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new ‘phylogenetic annotation’ process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources. PMID:23161678

  7. Functional Annotation of Rheumatoid Arthritis and Osteoarthritis Associated Genes by Integrative Genome-Wide Gene Expression Profiling Analysis

    PubMed Central

    Li, Zhan-Chun; Xiao, Jie; Peng, Jin-Liang; Chen, Jian-Wei; Ma, Tao; Cheng, Guang-Qi; Dong, Yu-Qi; Wang, Wei-li; Liu, Zu-De

    2014-01-01

    Background Rheumatoid arthritis (RA) and osteoarthritis (OA) are two major types of joint diseases that share multiple common symptoms. However, their pathological mechanism remains largely unknown. The aim of our study is to identify RA and OA related-genes and gain an insight into the underlying genetic basis of these diseases. Methods We collected 11 whole genome-wide expression profiling datasets from RA and OA cohorts and performed a meta-analysis to comprehensively investigate their expression signatures. This method can avoid some pitfalls of single dataset analyses. Results and Conclusion We found that several biological pathways (i.e., the immunity, inflammation and apoptosis related pathways) are commonly involved in the development of both RA and OA. Whereas several other pathways (i.e., vasopressin-related pathway, regulation of autophagy, endocytosis, calcium transport and endoplasmic reticulum stress related pathways) present significant difference between RA and OA. This study provides novel insights into the molecular mechanisms underlying this disease, thereby aiding the diagnosis and treatment of the disease. PMID:24551036

  8. MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data.

    PubMed

    Vallenet, David; Belda, Eugeni; Calteau, Alexandra; Cruveiller, Stéphane; Engelen, Stefan; Lajus, Aurélie; Le Fèvre, François; Longin, Cyrille; Mornico, Damien; Roche, David; Rouy, Zoé; Salvignol, Gregory; Scarpelli, Claude; Thil Smith, Adam Alexander; Weiman, Marion; Médigue, Claudine

    2013-01-01

    MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest. PMID:23193269

  9. Annotated chemical patent corpus: a gold standard for text mining.

    PubMed

    Akhondi, Saber A; Klenner, Alexander G; Tyrchan, Christian; Manchala, Anil K; Boppana, Kiran; Lowe, Daniel; Zimmermann, Marc; Jagarlapudi, Sarma A R P; Sayle, Roger; Kors, Jan A; Muresan, Sorel

    2014-01-01

    Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org. PMID:25268232

  10. Genome-Wide Annotation and Comparative Analysis of Cytochrome P450 Monooxygenases in Basidiomycete Biotrophic Plant Pathogens

    PubMed Central

    Sun, Yuxin; Letsimo, Elizabeth Mpholoseng; Parvez, Mohammad; Yu, Jae-Hyuk; Mashele, Samson Sitheni; Syed, Khajamohiddin

    2015-01-01

    Fungi are an exceptional source of diverse and novel cytochrome P450 monooxygenases (P450s), heme-thiolate proteins, with catalytic versatility. Agaricomycotina saprophytes have yielded most of the available information on basidiomycete P450s. This resulted in observing similar P450 family types in basidiomycetes with few differences in P450 families among Agaricomycotina saprophytes. The present study demonstrated the presence of unique P450 family patterns in basidiomycete biotrophic plant pathogens that could possibly have originated from the adaptation of these species to different ecological niches (host influence). Systematic analysis of P450s in basidiomycete biotrophic plant pathogens belonging to three different orders, Agaricomycotina (Armillaria mellea), Pucciniomycotina (Melampsora laricis-populina, M. lini, Mixia osmundae and Puccinia graminis) and Ustilaginomycotina (Ustilago maydis, Sporisorium reilianum and Tilletiaria anomala), revealed the presence of numerous putative P450s ranging from 267 (A. mellea) to 14 (M. osmundae). Analysis of P450 families revealed the presence of 41 new P450 families and 27 new P450 subfamilies in these biotrophic plant pathogens. Order-level comparison of P450 families between biotrophic plant pathogens revealed the presence of unique P450 family patterns in these organisms, possibly reflecting the characteristics of their order. Further comparison of P450 families with basidiomycete non-pathogens confirmed that biotrophic plant pathogens harbour the unique P450 families in their genomes. The CYP63, CYP5037, CYP5136, CYP5137 and CYP5341 P450 families were expanded in A. mellea when compared to other Agaricomycotina saprophytes and the CYP5221 and CYP5233 P450 families in P. graminis and M. laricis-populina. The present study revealed that expansion of these P450 families is due to paralogous evolution of member P450s. The presence of unique P450 families in these organisms serves as evidence of how a host

  11. Genome-Wide Annotation and Comparative Analysis of Cytochrome P450 Monooxygenases in Basidiomycete Biotrophic Plant Pathogens.

    PubMed

    Qhanya, Lehlohonolo Benedict; Matowane, Godfrey; Chen, Wanping; Sun, Yuxin; Letsimo, Elizabeth Mpholoseng; Parvez, Mohammad; Yu, Jae-Hyuk; Mashele, Samson Sitheni; Syed, Khajamohiddin

    2015-01-01

    Fungi are an exceptional source of diverse and novel cytochrome P450 monooxygenases (P450s), heme-thiolate proteins, with catalytic versatility. Agaricomycotina saprophytes have yielded most of the available information on basidiomycete P450s. This resulted in observing similar P450 family types in basidiomycetes with few differences in P450 families among Agaricomycotina saprophytes. The present study demonstrated the presence of unique P450 family patterns in basidiomycete biotrophic plant pathogens that could possibly have originated from the adaptation of these species to different ecological niches (host influence). Systematic analysis of P450s in basidiomycete biotrophic plant pathogens belonging to three different orders, Agaricomycotina (Armillaria mellea), Pucciniomycotina (Melampsora laricis-populina, M. lini, Mixia osmundae and Puccinia graminis) and Ustilaginomycotina (Ustilago maydis, Sporisorium reilianum and Tilletiaria anomala), revealed the presence of numerous putative P450s ranging from 267 (A. mellea) to 14 (M. osmundae). Analysis of P450 families revealed the presence of 41 new P450 families and 27 new P450 subfamilies in these biotrophic plant pathogens. Order-level comparison of P450 families between biotrophic plant pathogens revealed the presence of unique P450 family patterns in these organisms, possibly reflecting the characteristics of their order. Further comparison of P450 families with basidiomycete non-pathogens confirmed that biotrophic plant pathogens harbour the unique P450 families in their genomes. The CYP63, CYP5037, CYP5136, CYP5137 and CYP5341 P450 families were expanded in A. mellea when compared to other Agaricomycotina saprophytes and the CYP5221 and CYP5233 P450 families in P. graminis and M. laricis-populina. The present study revealed that expansion of these P450 families is due to paralogous evolution of member P450s. The presence of unique P450 families in these organisms serves as evidence of how a host

  12. Annotation and functional assignment of the genes for the C30 carotenoid pathways from the genomes of two bacteria: Bacillus indicus and Bacillus firmus.

    PubMed

    Steiger, Sabine; Perez-Fons, Laura; Cutting, Simon M; Fraser, Paul D; Sandmann, Gerhard

    2015-01-01

    Bacillus indicus and Bacillus firmus synthesize C30 carotenoids via farnesyl pyrophosphate, forming apophytoene as the first committed step in the pathway. The products of the pathways were methyl 4'-[6-O-acyl-glycosyl)oxy]-4,4'-diapolycopen-4-oic acid and 4,4'-diapolycopen-4,4'-dioic acid with putative glycosyl esters. The genomes of both bacteria were sequenced, and the genes for their early terpenoid and specific carotenoid pathways annotated. All genes for a functional 1-deoxy-d-xylulose 5-phosphate synthase pathway were identified in both species, whereas genes of the mevalonate pathway were absent. The genes for specific carotenoid synthesis and conversion were found on gene clusters which were organized differently in the two species. The genes involved in the formation of the carotenoid cores were assigned by functional complementation in Escherichia coli. This bacterium was co-transformed with a plasmid mediating the formation of the putative substrate and a second plasmid with the gene of interest. Carotenoid products in the transformants were determined by HPLC. Using this approach, we identified the genes for a 4,4'-diapophytoene synthase (crtM), 4,4'-diapophytoene desaturase (crtNa), 4,4'-diapolycopene ketolase (crtNb) and 4,4'-diapolycopene aldehyde oxidase (crtNc). The three crtN genes were closely related and belonged to the crtI gene family with a similar reaction mechanism of their enzyme products. Additional genes encoding glycosyltransferases and acyltransferases for the modification of the carotenoid skeleton of the diapolycopenoic acids were identified by comparison with the corresponding genes from other bacteria. PMID:25326460

  13. Ranking Biomedical Annotations with Annotator's Semantic Relevancy

    PubMed Central

    2014-01-01

    Biomedical annotation is a common and affective artifact for researchers to discuss, show opinion, and share discoveries. It becomes increasing popular in many online research communities, and implies much useful information. Ranking biomedical annotations is a critical problem for data user to efficiently get information. As the annotator's knowledge about the annotated entity normally determines quality of the annotations, we evaluate the knowledge, that is, semantic relationship between them, in two ways. The first is extracting relational information from credible websites by mining association rules between an annotator and a biomedical entity. The second way is frequent pattern mining from historical annotations, which reveals common features of biomedical entities that an annotator can annotate with high quality. We propose a weighted and concept-extended RDF model to represent an annotator, a biomedical entity, and their background attributes and merge information from the two ways as the context of an annotator. Based on that, we present a method to rank the annotations by evaluating their correctness according to user's vote and the semantic relevancy between the annotator and the annotated entity. The experimental results show that the approach is applicable and efficient even when data set is large. PMID:24899918

  14. Ranking biomedical annotations with annotator's semantic relevancy.

    PubMed

    Wu, Aihua

    2014-01-01

    Biomedical annotation is a common and affective artifact for researchers to discuss, show opinion, and share discoveries. It becomes increasing popular in many online research communities, and implies much useful information. Ranking biomedical annotations is a critical problem for data user to efficiently get information. As the annotator's knowledge about the annotated entity normally determines quality of the annotations, we evaluate the knowledge, that is, semantic relationship between them, in two ways. The first is extracting relational information from credible websites by mining association rules between an annotator and a biomedical entity. The second way is frequent pattern mining from historical annotations, which reveals common features of biomedical entities that an annotator can annotate with high quality. We propose a weighted and concept-extended RDF model to represent an annotator, a biomedical entity, and their background attributes and merge information from the two ways as the context of an annotator. Based on that, we present a method to rank the annotations by evaluating their correctness according to user's vote and the semantic relevancy between the annotator and the annotated entity. The experimental results show that the approach is applicable and efficient even when data set is large. PMID:24899918

  15. Facilitating functional annotation of chicken microarray data

    PubMed Central

    2009-01-01

    Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO). However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM) tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and will be updated on regular

  16. Quality of Computationally Inferred Gene Ontology Annotations

    PubMed Central

    Škunca, Nives; Altenhoff, Adrian; Dessimoz, Christophe

    2012-01-01

    Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon—an important outcome given that >98% of all annotations are inferred without direct curation. PMID:22693439

  17. Mitochondrial Disease Sequence Data Resource (MSeqDR): A global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities

    PubMed Central

    Falk, Marni J.; Shen, Lishuang; Gonzalez, Michael; Leipzig, Jeremy; Lott, Marie T.; Stassen, Alphons P.M.; Diroma, Maria Angela; Navarro-Gomez, Daniel; Yeske, Philip; Bai, Renkui; Boles, Richard G.; Brilhante, Virginia; Ralph, David; DaRe, Jeana T.; Shelton, Robert; Terry, Sharon; Zhang, Zhe; Copeland, William C.; van Oven, Mannis; Prokisch, Holger; Wallace, Douglas C.; Attimonelli, Marcella; Krotoski, Danuta; Zuchner, Stephan; Gai, Xiaowu

    2014-01-01

    Success rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires the establishment of robust data resources to enable data sharing that informs accurate understanding of genes, variants, and phenotypes. The “Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium” is a grass-roots effort facilitated by the United Mitochondrial Disease Foundation to identify and prioritize specific genomic data analysis needs of the global mitochondrial disease clinical and research community. A central Web portal (https://mseqdr.org) facilitates the coherent compilation, organization, annotation, and analysis of sequence data from both nuclear and mitochondrial genomes of individuals and families with suspected mitochondrial disease. This Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through use of a convenient distributed annotation system (DAS) mechanism. A range of data visualization and analysis tools are provided to facilitate user interrogation and understanding of genomic, and ultimately phenotypic, data of relevance to mitochondrial biology and disease. Currently available tools for nuclear and mitochondrial gene analyses include an MSeqDR GBrowse instance that hosts optimized mitochondrial disease and mitochondrial DNA (mtDNA) specific annotation tracks, as well as an MSeqDR locus-specific database (LSDB) that curates variant data on more than 1,300 genes that have been implicated in mitochondrial disease and/or encode mitochondria-localized proteins. MSeqDR is

  18. Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities.

    PubMed

    Falk, Marni J; Shen, Lishuang; Gonzalez, Michael; Leipzig, Jeremy; Lott, Marie T; Stassen, Alphons P M; Diroma, Maria Angela; Navarro-Gomez, Daniel; Yeske, Philip; Bai, Renkui; Boles, Richard G; Brilhante, Virginia; Ralph, David; DaRe, Jeana T; Shelton, Robert; Terry, Sharon F; Zhang, Zhe; Copeland, William C; van Oven, Mannis; Prokisch, Holger; Wallace, Douglas C; Attimonelli, Marcella; Krotoski, Danuta; Zuchner, Stephan; Gai, Xiaowu

    2015-03-01

    Success rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires the establishment of robust data resources to enable data sharing that informs accurate understanding of genes, variants, and phenotypes. The "Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium" is a grass-roots effort facilitated by the United Mitochondrial Disease Foundation to identify and prioritize specific genomic data analysis needs of the global mitochondrial disease clinical and research community. A central Web portal (https://mseqdr.org) facilitates the coherent compilation, organization, annotation, and analysis of sequence data from both nuclear and mitochondrial genomes of individuals and families with suspected mitochondrial disease. This Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through the use of a convenient distributed annotation system (DAS) mechanism. A range of data visualization and analysis tools are provided to facilitate user interrogation and understanding of genomic, and ultimately phenotypic, data of relevance to mitochondrial biology and disease. Currently available tools for nuclear and mitochondrial gene analyses include an MSeqDR GBrowse instance that hosts optimized mitochondrial disease and mitochondrial DNA (mtDNA) specific annotation tracks, as well as an MSeqDR locus-specific database (LSDB) that curates variant data on more than 1300 genes that have been implicated in mitochondrial disease and/or encode mitochondria-localized proteins. MSeqDR is

  19. Maize - GO annotation methods, evaluation, and review (Maize-GAMER)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Making a genome sequence accessible and useful involves three basic steps: genome assembly, structural annotation, and functional annotation. The quality of data generated at each step influences the accuracy of inferences that can be made, with high-quality analyses produce better datasets resultin...

  20. SpeedSeq: Ultra-fast personal genome analysis and interpretation

    PubMed Central

    Chiang, Colby; Layer, Ryan M.; Faust, Gregory G.; Lindberg, Michael R.; Rose, David B.; Garrison, Erik P.; Marth, Gabor T.; Quinlan, Aaron R.; Hall, Ira M.

    2015-01-01

    SpeedSeq is an open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 hours on a low-cost server, alleviating a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement. SpeedSeq offers competitive or superior performance to current methods for detecting germline and somatic single nucleotide variants, indels, and structural variants, and includes novel functionality for streamlined interpretation. PMID:26258291

  1. The Integrated Microbial Genomes (IMG) System: An Expanding Comparative Analysis Resource

    SciTech Connect

    Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Anderson, Iain; Lykidis, Athanasios; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

    2009-09-13

    The integrated microbial genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG contains both draft and complete microbial genomes integrated with other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through regular releases. Several companion IMG systems have been set up in order to serve domain specific needs, such as expert review of genome annotations. IMG is available at .

  2. Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.)

    PubMed Central

    Kim, Seungill; Kim, Myung-Shin; Kim, Yong-Min; Yeom, Seon-In; Cheong, Kyeongchae; Kim, Ki-Tae; Jeon, Jongbum; Kim, Sunggil; Kim, Do-Sun; Sohn, Seong-Han; Lee, Yong-Hwan; Choi, Doil

    2015-01-01

    The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp. PMID:25362073

  3. Descriptive Cataloging: A Selected, Annotated Bibliography, 1984-1985.

    ERIC Educational Resources Information Center

    Cook, C. Donald; Jones, Ellen

    1986-01-01

    This annotated bibliography of materials published during 1984-1985 on descriptive cataloging covers bibliographic control, Anglo American Cataloging Rules, 2nd edition (AACR2), specific types of materials, authority control, retrospective conversion, management issues, expert systems, and manuals. (EM)

  4. The RAST server : rapid annotations using subsystems technology.

    SciTech Connect

    Aziz, R. K.; Bartels, D.; Best, A. A.; DeJongh, M.; Disz, T.; Edwards, R. A.; Formsma, K.; Gerdes, S.; Glass, E. M.; Kubal, M.; Meyer, F.; Olsen, G. J.; Olson, R.; Osterman, A. L.; Overbeek, R. A.; McNeil, L. K.; Paarmann, D.; Paczian, T.; Parrello, B.; Pusch, G. D.; Reich, C.; Stevens, R.; Vassieva, O.; Vonstein, V.; Wilke, A.; Zagnitko, O.; Mathematics and Computer Science; Fellowship for Interpretation of Genomes; Univ. of Chicago; Univ. of Illinois; The Burnham Inst.; Hope Coll.; Univ. of Tenn.; Cairo Univ.

    2008-02-08

    The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12-24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service. By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.

  5. Protein Sequence Annotation Tool (PSAT): A centralized web-based meta-server for high-throughput sequence annotations

    DOE PAGESBeta

    Leung, Elo; Huang, Amy; Cadag, Eithon; Montana, Aldrin; Soliman, Jan Lorenz; Zhou, Carol L. Ecale

    2016-01-20

    In this study, we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resultingmore » functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. Lastly, PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/. PSAT stands apart from other sequencebased genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome.« less

  6. Analysis and Annotation of Nucleic Acid Sequence

    SciTech Connect

    States, David J.

    2004-07-28

    The aims of this project were to develop improved methods for computational genome annotation and to apply these methods to improve the annotation of genomic sequence data with a specific focus on human genome sequencing. The project resulted in a substantial body of published work. Notable contributions of this project were the identification of basecalling and lane tracking as error processes in genome sequencing and contributions to improved methods for these steps in genome sequencing. This technology improved the accuracy and throughput of genome sequence analysis. Probabilistic methods for physical map construction were developed. Improved methods for sequence alignment, alternative splicing analysis, promoter identification and NF kappa B response gene prediction were also developed.

  7. Analysis and Annotation of Nucleic Acid Sequence

    SciTech Connect

    David J. States

    1998-08-01

    The aims of this project were to develop improved methods for computational genome annotation and to apply these methods to improve the annotation of genomic sequence data with a specific focus on human genome sequencing. The project resulted in a substantial body of published work. Notable contributions of this project were the identification of basecalling and lane tracking as error processes in genome sequencing and contributions to improved methods for these steps in genome sequencing. This technology improved the accuracy and throughput of genome sequence analysis. Probabilistic methods for physical map construction were developed. Improved methods for sequence alignment, alternative splicing analysis, promoter identification and NF kappa B response gene prediction were also developed.

  8. Comparative genomic survey, exon-intron annotation and phylogenetic analysis of NAT-homologous sequences in archaea, protists, fungi, viruses, and invertebrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have previously published extensive genomic surveys [1-3], reporting NAT-homologous sequences in hundreds of sequenced bacterial, fungal and vertebrate genomes. We present here the results of our latest search of 2445 genomes, representing 1532 (70 archaeal, 1210 bacterial, 43 protist, 97 fungal,...

  9. MEETING: Chlamydomonas Annotation Jamboree - October 2003

    SciTech Connect

    Grossman, Arthur R

    2007-04-13

    Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) or individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual

  10. Joint stage recognition and anatomical annotation of drosophila gene expression patterns

    PubMed Central

    Cai, Xiao; Wang, Hua; Huang, Heng; Ding, Chris

    2012-01-01

    Motivation: Staining the mRNA of a gene via in situ hybridization (ISH) during the development of a Drosophila melanogaster embryo delivers the detailed spatio-temporal patterns of the gene expression. Many related biological problems such as the detection of co-expressed genes, co-regulated genes and transcription factor binding motifs rely heavily on the analysis of these image patterns. To provide the text-based pattern searching for facilitating related biological studies, the images in the Berkeley Drosophila Genome Project (BDGP) study are annotated with developmental stage term and anatomical ontology terms manually by domain experts. Due to the rapid increase in the number of such images and the inevitable bias annotations by human curators, it is necessary to develop an automatic method to recognize the developmental stage and annotate anatomical terms. Results: In this article, we propose a novel computational model for jointly stage classification and anatomical terms annotation of Drosophila gene expression patterns. We propose a novel Tri-Relational Graph (TG) model that comprises the data graph, anatomical term graph, developmental stage term graph, and connect them by two additional graphs induced from stage or annotation label assignments. Upon the TG model, we introduce a Preferential Random Walk (PRW) method to jointly recognize developmental stage and annotate anatomical terms by utilizing the interrelations between two tasks. The experimental results on two refined BDGP datasets demonstrate that our joint learning method can achieve superior prediction results on both tasks than the state-of-the-art methods. Availability: http://ranger.uta.edu/%7eheng/Drosophila/ Contact: heng@uta.edu PMID:22689756

  11. Functional annotation of hypothetical proteins – A review

    PubMed Central

    Sivashankari, Selvarajan; Shanmughavel, Piramanayagam

    2006-01-01

    The complete human genome sequences in the public database provide ways to understand the blue print of life. As of June 29, 2006, 27 archaeal, 326 bacterial and 21 eukaryotes is complete genomes are available and the sequencing for 316 bacterial, 24 archaeal, 126 eukaryotic genomes are in progress. The traditional biochemical/molecular experiments can assign accurate functions for genes in these genomes. However, the process is time-consuming and costly. Despite several efforts, only 50-60 % of genes have been annotated in most completely sequenced genomes. Automated genome sequence analysis and annotation may provide ways to understand genomes. Thus, determination of protein function is one of the challenging problems of the post-genome era. This demands bioinformatics to predict functions of un-annotated protein sequences by developing efficient tools. Here, we discuss some of the recent and popular approaches developed in Bioinformatics to predict functions for hypothetical proteins. PMID:17597916

  12. Annotations in Refseq (GSC8 Meeting)

    ScienceCinema

    Tatusova, Tatiana

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Tatiana Tatusova of NCBI discusses "Annotations in Refseq" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009.

  13. Annotations in Refseq (GSC8 Meeting)

    SciTech Connect

    Tatusova, Tatiana

    2009-09-10

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Tatiana Tatusova of NCBI discusses "Annotations in Refseq" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009.

  14. Automated annotation of microbial proteomes in SWISS-PROT.

    PubMed

    Gattiker, Alexandre; Michoud, Karine; Rivoire, Catherine; Auchincloss, Andrea H; Coudert, Elisabeth; Lima, Tania; Kersey, Paul; Pagni, Marco; Sigrist, Christian J A; Lachaize, Corinne; Veuthey, Anne Lise; Gasteiger, Elisabeth; Bairoch, Amos

    2003-02-01

    Large-scale sequencing of prokaryotic genomes demands the automation of certain annotation tasks currently manually performed in the production of the SWISS-PROT protein knowledgebase. The HAMAP project, or 'High-quality Automated and Manual Annotation of microbial Proteomes', aims to integrate manual and automatic annotation methods in order to enhance the speed of the curation process while preserving the quality of the database annotation. Automatic annotation is only applied to entries that belong to manually defined orthologous families and to entries with no identifiable similarities (ORFans). Many checks are enforced in order to prevent the propagation of wrong annotation and to spot problematic cases, which are channelled to manual curation. The results of this annotation are integrated in SWISS-PROT, and a website is provided at http://www.expasy.org/sprot/hamap/. PMID:12798039

  15. Draft Genome Sequence and Annotation of Phyllosphere-Persisting Salmonella enterica subsp. enterica Serovar Livingstone Strain CKY-S4, Isolated from an Urban Lake in Regina, Canada.

    PubMed

    Tambalo, Dinah D; Perry, Benjamin J; Fitzgerald, Stephen F; Cameron, Andrew D S; Yost, Christopher K

    2015-01-01

    Here, we report the first draft genome sequence of Salmonella enterica subsp. enterica serovar Livingstone. This S. Livingstone strain CKY-S4 displayed biofilm formation and cellulose production and could persist on lettuce. This genome may help the study of mechanisms by which enteric pathogens colonize food crops. PMID:26272568

  16. Draft Genome Sequence and Annotation of Phyllosphere-Persisting Salmonella enterica subsp. enterica Serovar Livingstone Strain CKY-S4, Isolated from an Urban Lake in Regina, Canada

    PubMed Central

    Tambalo, Dinah D.; Perry, Benjamin J.; Fitzgerald, Stephen F.; Cameron, Andrew D. S.

    2015-01-01

    Here, we report the first draft genome sequence of Salmonella enterica subsp. enterica serovar Livingstone. This S. Livingstone strain CKY-S4 displayed biofilm formation and cellulose production and could persist on lettuce. This genome may help the study of mechanisms by which enteric pathogens colonize food crops. PMID:26272568

  17. CRISPRdigger: detecting CRISPRs with better direct repeat annotations

    PubMed Central

    Ge, Ruiquan; Mai, Guoqin; Wang, Pu; Zhou, Manli; Luo, Youxi; Cai, Yunpeng; Zhou, Fengfeng

    2016-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPRs) are important genetic elements in many bacterial and archaeal genomes, and play a key role in prokaryote immune systems’ fight against invasive foreign elements. The CRISPR system has also been engineered to facilitate target gene editing in eukaryotic genomes. Using the common features of mis-annotated CRISPRs in prokaryotic genomes, this study proposed an accurate de novo CRISPR annotation program CRISPRdigger, which can take a partially assembled genome as its input. A comprehensive comparison with the three existing programs demonstrated that CRISPRdigger can recover more Direct Repeats (DRs) for CRISPRs and achieve a higher accuracy for a query genome. The program was implemented by Perl and all the parameters had default values, so that a user could annotate CRISPRs in a query genome by supplying only a genome sequence in the FASTA format. All the supplementary data are available at http://www.healthinformaticslab.org/supp/. PMID:27596864

  18. CRISPRdigger: detecting CRISPRs with better direct repeat annotations.

    PubMed

    Ge, Ruiquan; Mai, Guoqin; Wang, Pu; Zhou, Manli; Luo, Youxi; Cai, Yunpeng; Zhou, Fengfeng

    2016-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPRs) are important genetic elements in many bacterial and archaeal genomes, and play a key role in prokaryote immune systems' fight against invasive foreign elements. The CRISPR system has also been engineered to facilitate target gene editing in eukaryotic genomes. Using the common features of mis-annotated CRISPRs in prokaryotic genomes, this study proposed an accurate de novo CRISPR annotation program CRISPRdigger, which can take a partially assembled genome as its input. A comprehensive comparison with the three existing programs demonstrated that CRISPRdigger can recover more Direct Repeats (DRs) for CRISPRs and achieve a higher accuracy for a query genome. The program was implemented by Perl and all the parameters had default values, so that a user could annotate CRISPRs in a query genome by supplying only a genome sequence in the FASTA format. All the supplementary data are available at http://www.healthinformaticslab.org/supp/. PMID:27596864

  19. Representing annotation compositionality and provenance for the Semantic Web

    PubMed Central

    2013-01-01

    Background Though the annotation of digital artifacts with metadata has a long history, the bulk of that work focuses on the association of single terms or concepts to single targets. As annotation efforts expand to capture more complex information, annotations will need to be able to refer to knowledge structures formally defined in terms of more atomic knowledge structures. Existing provenance efforts in the Semantic Web domain primarily focus on tracking provenance at the level of whole triples and do not provide enough detail to track how individual triple elements of annotations were derived from triple elements of other annotations. Results We present a task- and domain-independent ontological model for capturing annotations and their linkage to their denoted knowledge representations, which can be singular concepts or more complex sets of assertions. We have implemented this model as an extension of the Information Artifact Ontology in OWL and made it freely available, and we show how it can be integrated with several prominent annotation and provenance models. We present several application areas for the model, ranging from linguistic annotation of text to the annotation of disease-associations in genome sequences. Conclusions With this model, progressively more complex annotations can be composed from other annotations, and the provenance of compositional annotations can be represented at the annotation level or at the level of individual elements of the RDF triples composing the annotations. This in turn allows for progressively richer annotations to be constructed from previous annotation efforts, the precise provenance recording of which facilitates evidence-based inference and error tracking. PMID:24268021

  20. Cancer markers: integratively annotated classification.

    PubMed

    Orsini, M; Travaglione, A; Capobianco, E

    2013-11-10

    Translational cancer genomics research aims to ensure that experimental knowledge is subject to computational analysis, and integrated with a variety of records from omics and clinical sources. The data retrieval from such sources is not trivial, due to their redundancy and heterogeneity, and the presence of false evidence. In silico marker identification, therefore, remains a complex task that is mainly motivated by the impact that target identification from the elucidation of gene co-expression dynamics and regulation mechanisms, combined with the discovery of genotype-phenotype associations, may have for clinical validation. Based on the reuse of publicly available gene expression data, our aim is to propose cancer marker classification by integrating the prediction power of multiple annotation sources. In particular, with reference to the functional annotation for colorectal markers, we indicate a classification of markers into diagnostic and prognostic classes combined with susceptibility and risk factors. PMID:23928109

  1. Towards a Consensus Annotation System (GSC8 Meeting)

    SciTech Connect

    White, Owen

    2009-09-10

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. "Comparing Annotations: Towards Consensus Annotation" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009

  2. Towards a Consensus Annotation System (GSC8 Meeting)

    ScienceCinema

    White, Owen [University of Maryland

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. "Comparing Annotations: Towards Consensus Annotation" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009

  3. Genotator: a workbench for sequence annotation.

    PubMed

    Harris, N L

    1997-07-01

    Sequencing centers such as the Human Genome Center at LBNL are producing an ever-increasing flood of genetic data. Annotation can greatly enhance the biological value of these sequences. Useful annotations include possible gene locations, homologies to known genes, and gene signal such as promoters and splice sites. Genotator is a workbench for automated sequence annotation and annotation browsing. The back end runs a series of sequence analysis tools on a DNA sequence, handling the various input and output formats required by the tools. Genotator currently runs five different gene-finding programs, three homology searches, and searches for promoters, splice sites, and ORFs. The results of the analyses run by Genotator can be viewed with the interactive graphical browser. The browser displays color-coded sequence annotations on a canvas that can be scrolled and zoomed, allowing the annotated sequence to be explored at multiple levels of detail. The user can view the actual DNA sequence in a separate window; when a region is selected in the map display, it is highlighted automatically in the sequence display, and vice versa. By displaying the output of all of the sequence analyses, Genotator provides an intuitive way to identify the significant regions (for example, probable exons) in a sequence. Users can interactively add personal annotations to label regions of interest. Additional capabilities of Genotator include primer design and pattern searching. PMID:9253604

  4. Gene and alternative splicing annotation with AIR

    PubMed Central

    Florea, Liliana; Di Francesco, Valentina; Miller, Jason; Turner, Russell; Yao, Alison; Harris, Michael; Walenz, Brian; Mobarry, Clark; Merkulov, Gennady V.; Charlab, Rosane; Dew, Ian; Deng, Zuoming; Istrail, Sorin; Li, Peter; Sutton, Granger

    2005-01-01

    Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We present a methodology for the automated annotation of genes and their alternatively spliced mRNA transcripts based on existing cDNA and protein sequence evidence from the same species or projected from a related species using syntenic mapping information. At the core of the method is the splice graph, a compact representation of a gene, its exons, introns, and alternatively spliced isoforms. The putative transcripts are enumerated from the graph and assigned confidence scores based on the strength of sequence evidence, and a subset of the high-scoring candidates are selected and promoted into the annotation. The method is highly selective, eliminating the unlikely candidates while retaining 98% of the high-quality mRNA evidence in well-formed transcripts, and produces annotation that is measurably more accurate than some evidence-based gene sets. The process is fast, accurate, and fully automated, and combines the traditionally distinct gene annotation and alternative splicing detection processes in a comprehensive and systematic way, thus considerably aiding in the ensuing manual curation efforts. PMID:15632090

  5. High-Quality Genome Assembly and Annotation for Plasmodium coatneyi, Generated Using Single-Molecule Real-Time PacBio Technology

    PubMed Central

    Chien, Jung-Ting; Pakala, Suman B.; Geraldo, Juliana A.; Lapp, Stacey A.; Humphrey, Jay C.; Barnwell, John W.; Kissinger, Jessica C.

    2016-01-01

    Plasmodium coatneyi is a protozoan parasite species that causes simian malaria and is an excellent model for studying disease caused by the human malaria parasite, P. falciparum. Here we report the complete (nontelomeric) genome sequence of P. coatneyi Hackeri generated by the application of only Pacific Biosciences RS II (PacBio RS II) single-molecule real-time (SMRT) high-resolution sequence technology and assembly using the Hierarchical Genome Assembly Process (HGAP). This is the first Plasmodium genome sequence reported to use only PacBio technology. This approach has proven to be superior to short-read only approaches for this species. PMID:27587810

  6. High-Quality Genome Assembly and Annotation for Plasmodium coatneyi, Generated Using Single-Molecule Real-Time PacBio Technology.

    PubMed

    Chien, Jung-Ting; Pakala, Suman B; Geraldo, Juliana A; Lapp, Stacey A; Humphrey, Jay C; Barnwell, John W; Kissinger, Jessica C; Galinski, Mary R

    2016-01-01

    Plasmodium coatneyi is a protozoan parasite species that causes simian malaria and is an excellent model for studying disease caused by the human malaria parasite, P. falciparum Here we report the complete (nontelomeric) genome sequence of P. coatneyi Hackeri generated by the application of only Pacific Biosciences RS II (PacBio RS II) single-molecule real-time (SMRT) high-resolution sequence technology and assembly using the Hierarchical Genome Assembly Process (HGAP). This is the first Plasmodium genome sequence reported to use only PacBio technology. This approach has proven to be superior to short-read only approaches for this species. PMID:27587810

  7. Expert Biogeographers

    ERIC Educational Resources Information Center

    Bednarski, Marsha

    2006-01-01

    This article describes an alternative way of teaching about biomes by having students become expert biogeographers. In order to become experts students need to first find out what a biogeographer does. Doing an online search lets students find out for themselves what the responsibilities are of people who work in this field. A good place to visit…

  8. k-merSNP discovery: Software for alignment-and reference-free scalable SNP discovery, phylogenetics, and annotation for hundreds of microbial genomes

    SciTech Connect

    2014-11-18

    With the flood of whole genome finished and draft microbial sequences, we need faster, more scalable bioinformatics tools for sequence comparison. An algorithm is described to find single nucleotide polymorphisms (SNPs) in whole genome data. It scales to hundreds of bacterial or viral genomes, and can be used for finished and/or draft genomes available as unassembled contigs or raw, unassembled reads. The method is fast to compute, finding SNPs and building a SNP phylogeny in minutes to hours, depending on the size and diversity of the input sequences. The SNP-based trees that result are consistent with known taxonomy and trees determined in other studies. The approach we describe can handle many gigabases of sequence in a single run. The algorithm is based on k-mer analysis.

  9. k-merSNP discovery: Software for alignment-and reference-free scalable SNP discovery, phylogenetics, and annotation for hundreds of microbial genomes

    Energy Science and Technology Software Center (ESTSC)

    2014-11-18

    With the flood of whole genome finished and draft microbial sequences, we need faster, more scalable bioinformatics tools for sequence comparison. An algorithm is described to find single nucleotide polymorphisms (SNPs) in whole genome data. It scales to hundreds of bacterial or viral genomes, and can be used for finished and/or draft genomes available as unassembled contigs or raw, unassembled reads. The method is fast to compute, finding SNPs and building a SNP phylogeny inmore » minutes to hours, depending on the size and diversity of the input sequences. The SNP-based trees that result are consistent with known taxonomy and trees determined in other studies. The approach we describe can handle many gigabases of sequence in a single run. The algorithm is based on k-mer analysis.« less

  10. Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation

    PubMed Central

    2013-01-01

    Background The Streptococcus Anginosus Group (SAG) represents three closely related species of the viridans group streptococci recognized as commensal bacteria of the oral, gastrointestinal and urogenital tracts. The SAG also cause severe invasive infections, and are pathogens during cystic fibrosis (CF) pulmonary exacerbation. Little genomic information or description of virulence mechanisms is currently available for SAG. We conducted intra and inter species whole-genome comparative analyses with 59 publically available Streptococcus genomes and seven in-house closed high quality finished SAG genomes; S. constellatus (3), S. intermedius (2), and S. anginosus (2). For each SAG species, we sequenced at least one numerically dominant strain from CF airways recovered during acute exacerbation and an invasive, non-lung isolate. We also evaluated microevolution that occurred within two isolates that were cultured from one individual one year apart. Results The SAG genomes were most closely related to S. gordonii and S. sanguinis, based on shared orthologs and harbor a similar number of proteins within each COG category as other Streptococcus species. Numerous characterized streptococcus virulence factor homologs were identified within the SAG genomes including; adherence, invasion, spreading factors, LPxTG cell wall proteins, and two component histidine kinases known to be involved in virulence gene regulation. Mobile elements, primarily integrative conjugative elements and bacteriophage, account for greater than 10% of the SAG genomes. S. anginosus was the most variable species sequenced in this study, yielding both the smallest and the largest SAG genomes containing multiple genomic rearrangements, insertions and deletions. In contrast, within the S. constellatus and S. intermedius species, there was extensive continuous synteny, with only slight differences in genome size between strains. Within S. constellatus we were able to determine important SNPs and changes in

  11. Genome-wide Annotation and Comparative Analysis of Long Terminal Repeat Retrotransposons between Pear Species of P. bretschneideri and P. Communis

    PubMed Central

    Yin, Hao; Du, Jianchang; Wu, Jun; Wei, Shuwei; Xu, Yingxiu; Tao, Shutian; Wu, Juyou; Zhang, Shaoling

    2015-01-01

    Recent sequencing of the Oriental pear (P. bretschneideri Rehd.) genome and the availability of the draft genome sequence of Occidental pear (P. communis L.), has provided a good opportunity to characterize the abundance, distribution, timing, and evolution of long terminal repeat retrotransposons (LTR-RTs) in these two important fruit plants. Here, a total of 7247 LTR-RTs, which can be classified into 148 families, have been identified in the assembled Oriental pear genome. Unlike in other plant genomes, approximately 90% of these elements were found to be randomly distributed along the pear chromosomes. Further analysis revealed that the amplification timeframe of elements varies dramatically in different families, super-families and lineages, and the Copia-like elements have highest activity in the recent 0.5 million years (Mys). The data also showed that two genomes evolved with similar evolutionary rates after their split from the common ancestor ~0.77–1.66 million years ago (Mya). Overall, the data provided here will be a valuable resource for further investigating the impact of transposable elements on gene structure, expression, and epigenetic modification in the pear genomes. PMID:26631625

  12. Expert Seeker

    NASA Technical Reports Server (NTRS)

    Fernandez, Becerra

    2003-01-01

    Expert Seeker is a computer program of the knowledge-management-system (KMS) type that falls within the category of expertise-locator systems. The main goal of the KMS system implemented by Expert Seeker is to organize and distribute knowledge of who are the domain experts within and without a given institution, company, or other organization. The intent in developing this KMS was to enable the re-use of organizational knowledge and provide a methodology for querying existing information (including structured, semistructured, and unstructured information) in a way that could help identify organizational experts. More specifically, Expert Seeker was developed to make it possible, by use of an intranet, to do any or all of the following: Assist an employee in identifying who has the skills needed for specific projects and to determine whether the experts so identified are available. Assist managers in identifying employees who may need training opportunities. Assist managers in determining what expertise is lost when employees retire or otherwise leave. Facilitate the development of new ways of identifying opportunities for innovation and minimization of duplicated efforts. Assist employees in achieving competitive advantages through the application of knowledge-management concepts and related systems. Assist external organizations in requesting speakers for specific engagements or determining from whom they might be able to request help via electronic mail. Help foster an environment of collaboration for rapid development in today's environment, in which it is increasingly necessary to assemble teams of experts from government, universities, research laboratories, and industries, to quickly solve problems anytime, anywhere. Make experts more visible. Provide a central repository of information about employees, including information that, heretofore, has typically not been captured by the human-resources systems (e.g., information about past projects, patents, or

  13. Computing human image annotation.

    PubMed

    Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Rubin, Daniel L

    2009-01-01

    An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human (or machine) observer. An image markup is the graphical symbols placed over the image to depict an annotation. In the majority of current, clinical and research imaging practice, markup is captured in proprietary formats and annotations are referenced only in free text radiology reports. This makes these annotations difficult to query, retrieve and compute upon, hampering their integration into other data mining and analysis efforts. This paper describes the National Cancer Institute's Cancer Biomedical Informatics Grid's (caBIG) Annotation and Image Markup (AIM) project, focusing on how to use AIM to query for annotations. The AIM project delivers an information model for image annotation and markup. The model uses controlled terminologies for important concepts. All of the classes and attributes of the model have been harmonized with the other models and common data elements in use at the National Cancer Institute. The project also delivers XML schemata necessary to instantiate AIMs in XML as well as a software application for translating AIM XML into DICOM S/R and HL7 CDA. Large collections of AIM annotations can be built and then queried as Grid or Web services. Using the tools of the AIM project, image annotations and their markup can be captured and stored in human and machine readable formats. This enables the inclusion of human image observation and inference as part of larger data mining and analysis activities. PMID:19964202

  14. The GATO gene annotation tool for research laboratories.

    PubMed

    Fujita, A; Massirer, K B; Durham, A M; Ferreira, C E; Sogayar, M C

    2005-11-01

    Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB. PMID:16258624

  15. Global probabilistic annotation of metabolic networks enables enzyme discovery

    PubMed Central

    Plata, Germán; Fuhrer, Tobias; Hsiao, Tzu-Lin; Sauer, Uwe; Vitkup, Dennis

    2013-01-01

    Annotation of organism-specific metabolic networks is one of the main challenges of systems biology. Importantly, due to inherent uncertainty of computational annotations, predictions of biochemical function need to be treated probabilistically. We present a global probabilistic approach to annotate genome-scale metabolic networks that integrates sequence homology and context-based correlations under a single principled framework. The developed method for Global Biochemical reconstruction Using Sampling (GLOBUS) not only provides annotation probabilities for each functional assignment, but also suggests likely alternative functions. GLOBUS is based on statistical Gibbs sampling of probable metabolic annotations and is able to make accurate functional assignments even in cases of remote sequence identity to known enzymes. We apply GLOBUS to genomes of Bacillus subtilis and Staphylococcus aureus, and validate the method predictions by experimentally demonstrating the 6-phosphogluconolactonase activity of ykgB and the role of the sps pathway for rhamnose biosynthesis in B. subtilis. PMID:22960854

  16. Genome sequence and annotation of Trichoderma parareesei, the ancestor of the cellulase producer Trichoderma reesei

    SciTech Connect

    Yang, Dongqing; Pomraning, Kyle; Kopchinskiy, Alexey; Karimi, Aghcheh Razieh; Atanasova, Lea; Chenthamara, Komal; Baker, Scott E.; Zhang, Ruifu; Shen, Qirong; Freitag, Michael; Kubicek, Christian P.; Druzhinina, Irina S.

    2015-08-13

    The filamentous fungus Trichoderma parareesei is the asexually reproducing ancestor of Trichoderma reesei, the holomorphic industrial producer of cellulase and hemicellulase. Here, we present the genome sequence of the T. parareesei type strain CBS 125925, which contains genes for 9,318 proteins.

  17. PhytoPath: an integrative resource for plant pathogen genomics.

    PubMed

    Pedro, Helder; Maheswari, Uma; Urban, Martin; Irvine, Alistair George; Cuzick, Alayne; McDowall, Mark D; Staines, Daniel M; Kulesha, Eugene; Hammond-Kosack, Kim Elizabeth; Kersey, Paul Julian

    2016-01-01

    PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the Ensembl tools for data visualization and analysis. The resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated. Genes with associated PHI-base data can be easily identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser. The PhytoPath resource contains data for 135 genomic sequences from 87 plant pathogen species, and 1364 genes curated for their role in pathogenicity and as targets for chemical intervention. Support for community annotation of gene models is provided using the WebApollo online gene editor, and we are working with interested communities to improve reference annotation for selected species. PMID:26476449

  18. PhytoPath: an integrative resource for plant pathogen genomics

    PubMed Central

    Pedro, Helder; Maheswari, Uma; Urban, Martin; Irvine, Alistair George; Cuzick, Alayne; McDowall, Mark D.; Staines, Daniel M.; Kulesha, Eugene; Hammond-Kosack, Kim Elizabeth; Kersey, Paul Julian

    2016-01-01

    PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the Ensembl tools for data visualization and analysis. The resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated. Genes with associated PHI-base data can be easily identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser. The PhytoPath resource contains data for 135 genomic sequences from 87 plant pathogen species, and 1364 genes curated for their role in pathogenicity and as targets for chemical intervention. Support for community annotation of gene models is provided using the WebApollo online gene editor, and we are working with interested communities to improve reference annotation for selected species. PMID:26476449

  19. ORegAnno: an open-access community-driven resource for regulatory annotation

    PubMed Central

    Griffith, Obi L.; Montgomery, Stephen B.; Bernier, Bridget; Chu, Bryan; Kasaian, Katayoon; Aerts, Stein; Mahony, Shaun; Sleumer, Monica C.; Bilenky, Mikhail; Haeussler, Maximilian; Griffith, Malachi; Gallo, Steven M.; Giardine, Belinda; Hooghe, Bart; Van Loo, Peter; Blanco, Enrique; Ticoll, Amy; Lithwick, Stuart; Portales-Casamar, Elodie; Donaldson, Ian J.; Robertson, Gordon; Wadelius, Claes; De Bleser, Pieter; Vlieghe, Dominique; Halfon, Marc S.; Wasserman, Wyeth; Hardison, Ross; Bergman, Casey M.; Jones, Steven J.M.

    2008-01-01

    ORegAnno is an open-source, open-access database and literature curation system for community-based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. The current release comprises 30 145 records curated from 922 publications and describing regulatory sequences for over 3853 genes and 465 transcription factors from 19 species. A new feature called the ‘publication queue’ allows users to input relevant papers from scientific literature as targets for annotation. The queue contains 4438 gene regulation papers entered by experts and another 54 351 identified by text-mining methods. Users can enter or ‘check out’ papers from the queue for manual curation using a series of user-friendly annotation pages. A typical record entry consists of species, sequence type, sequence, target gene, binding factor, experimental outcome and one or more lines of experimental evidence. An evidence ontology was developed to describe and categorize these experiments. Records are cross-referenced to Ensembl or Entrez gene identifiers, PubMed and dbSNP and can be visualized in the Ensembl or UCSC genome browsers. All data are freely available through search pages, XML data dumps or web services at: http://www.oreganno.org. PMID:18006570

  20. A Novel Approach to Semantic and Coreference Annotation at LLNL

    SciTech Connect

    Firpo, M

    2005-02-04

    A case is made for the importance of high quality semantic and coreference annotation. The challenges of providing such annotation are described. Asperger's Syndrome is introduced, and the connections are drawn between the needs of text annotation and the abilities of persons with Asperger's Syndrome to meet those needs. Finally, a pilot program is recommended wherein semantic annotation is performed by people with Asperger's Syndrome. The primary points embodied in this paper are as follows: (1) Document annotation is essential to the Natural Language Processing (NLP) projects at Lawrence Livermore National Laboratory (LLNL); (2) LLNL does not currently have a system in place to meet its need for text annotation; (3) Text annotation is challenging for a variety of reasons, many related to its very rote nature; (4) Persons with Asperger's Syndrome are particularly skilled at rote verbal tasks, and behavioral experts agree that they would excel at text annotation; and (6) A pilot study is recommend in which two to three people with Asperger's Syndrome annotate documents and then the quality and throughput of their work is evaluated relative to that of their neuro-typical peers.

  1. SEED Software Annotations.

    ERIC Educational Resources Information Center

    Bethke, Dee; And Others

    This document provides a composite index of the first five sets of software annotations produced by Project SEED. The software has been indexed by title, subject area, and grade level, and it covers sets of annotations distributed in September 1986, April 1987, September 1987, November 1987, and February 1988. The date column in the index…

  2. Biosynthesis of Akaeolide and Lorneic Acids and Annotation of Type I Polyketide Synthase Gene Clusters in the Genome of Streptomyces sp. NPS554

    PubMed Central

    Zhou, Tao; Komaki, Hisayuki; Ichikawa, Natsuko; Hosoyama, Akira; Sato, Seizo; Igarashi, Yasuhiro

    2015-01-01

    The incorporation pattern of biosynthetic precursors into two structurally unique polyketides, akaeolide and lorneic acid A, was elucidated by feeding experiments with 13C-labeled precursors. In addition, the draft genome sequence of the producer, Streptomyces sp. NPS554, was performed and the biosynthetic gene clusters for these polyketides were identified. The putative gene clusters contain all the polyketide synthase (PKS) domains necessary for assembly of the carbon skeletons. Combined with the 13C-labeling results, gene function prediction enabled us to propose biosynthetic pathways involving unusual carbon-carbon bond formation reactions. Genome analysis also indicated the presence of at least ten orphan type I PKS gene clusters that might be responsible for the production of new polyketides. PMID:25603349

  3. WEGO: a web tool for plotting GO annotations.

    PubMed

    Ye, Jia; Fang, Lin; Zheng, Hongkun; Zhang, Yong; Chen, Jie; Zhang, Zengjin; Wang, Jing; Li, Shengting; Li, Ruiqiang; Bolund, Lars; Wang, Jun

    2006-07-01

    Unified, structured vocabularies and classifications freely provided by the Gene Ontology (GO) Consortium are widely accepted in most of the large scale gene annotation projects. Consequently, many tools have been created for use with the GO ontologies. WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO annotation results. Different from other commercial software for creating chart, WEGO is designed to deal with the directed acyclic graph structure of GO to facilitate histogram creation of GO annotation results. WEGO has been used widely in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the daily tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. WEGO, along with the two other tools, namely External to GO Query and GO Archive Query, are freely available for all users at http://wego.genomics.org.cn. There are two available mirror sites at http://wego2.genomics.org.cn and http://wego.genomics.com.cn. Any suggestions are welcome at wego@genomics.org.cn. PMID:16845012

  4. Annotated Genome Sequence of Mycobacterium massiliense Strain M154, Belonging to the Recently Created Taxon Mycobacterium abscessus subsp. bolletii comb. nov.

    PubMed Central

    Wong, Yan Ling; Tan, Joon Liang; Ong, Chia Sui; Wong, Guat Jah; Ng, Kee Peng

    2012-01-01

    Mycobacterium massiliense has recently been proposed as a member of Mycobacterium abscessus subsp. bolletii comb. nov. Strain M154, a clinical isolate from the bronchoalveolar lavage fluid of a Malaysian patient presenting with lower respiratory tract infection, was subjected to shotgun DNA sequencing with the Illumina sequencing technology to obtain whole-genome sequence data for comparison with other genetically related strains within the M. abscessus species complex. PMID:22887675

  5. PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation

    PubMed Central

    Lenz, Henning; Knoop, Volker

    2013-01-01

    RNA editing is vast in some genetic systems, with up to thousands of targeted C-to-U and U-to-C substitutions in mitochondria and chloroplasts of certain plants. Efficient prognoses of RNA editing in organelle genomes will help to reveal overlooked cases of editing. We present PREPACT 2.0 (http://www.prepact.de) with numerous enhancements of our previously developed Plant RNA Editing Prediction & Analysis Computer Tool. Reference organelle transcriptomes for editing prediction have been extended and reorganized to include 19 curated mitochondrial and 13 chloroplast genomes, now allowing to distinguish RNA editing sites from “pre-edited” sites. Queries may be run against multiple references and a new “commons” function identifies and highlights orthologous candidate editing sites congruently predicted by multiple references. Enhancements to the BLASTX mode in PREPACT 2.0 allow querying of complete novel organelle genomes within a few minutes, identifying protein genes and candidate RNA editing sites simultaneously without prior user analyses. PMID:23362369

  6. The annotated complete DNA sequence of Enterococcus faecalis bacteriophage φEf11 and its comparison with all available phage and predicted prophage genomes.

    PubMed

    Stevens, Roy H; Ektefaie, Mahmoud R; Fouts, Derrick E

    2011-04-01

    φEf11 is a temperate Siphoviridae bacteriophage isolated by induction from a lysogenic Enterococcus faecalis strain. The φEf11 DNA was completely sequenced and found to be 42,822 bp in length, with a G+C mol% of 34.4%. Genome analysis revealed 65 ORFs, accounting for 92.8% of the DNA content. All except for seven of the ORFs displayed sequence similarities to previously characterized proteins. The genes were arranged in functional modules, organized similar to that of several other phages of low GC Gram-positive bacteria; however, the number and arrangement of lysis-related genes were atypical of these bacteriophages. A 159 bp noncoding region between predicted cI and cro genes is highly similar to the functionally characterized early promoter region of lactococcal temperate phage TP901-1, and possessed a predicted stem-loop structure in between predicted P(L) and P(R) promoters, suggesting a novel mechanism of repression of these two bacteriophages from the λ paradigm. Comparison with all available phage and predicted prophage genomes revealed that the φEf11 genome displays unique features, suggesting that φEf11 may be a novel member of a larger family of temperate prophages that also includes lactococcal phages. Trees based on the blast score ratio grouped this family by tail fiber similarity, suggesting that these trees are useful for identifying phages with similar tail fibers. PMID:21204936

  7. Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX

    PubMed Central

    Martínez Barrio, Álvaro; Lagercrantz, Erik; Sperber, Göran O; Blomberg, Jonas; Bongcam-Rudloff, Erik

    2009-01-01

    Background The Distributed Annotation System (DAS) is a widely used network protocol for sharing biological information. The distributed aspects of the protocol enable the use of various reference and annotation servers for connecting biological sequence data to pertinent annotations in order to depict an integrated view of the data for the final user. Results An annotation server has been devised to provide information about the endogenous retroviruses detected and annotated by a specialized in silico tool called RetroTector. We describe the procedure to implement the DAS 1.5 protocol commands necessary for constructing the DAS annotation server. We use our server to exemplify those steps. Data distribution is kept separated from visualization which is carried out by eBioX, an easy to use open source program incorporating multiple bioinformatics utilities. Some well characterized endogenous retroviruses are shown in two different DAS clients. A rapid analysis of areas free from retroviral insertions could be facilitated by our annotations. Conclusion The DAS protocol has shown to be advantageous in the distribution of endogenous retrovirus data. The distributed nature of the protocol is also found to aid in combining annotation and visualization along a genome in order to enhance the understanding of ERV contribution to its evolution. Reference and annotation servers are conjointly used by eBioX to provide visualization of ERV annotations as well as other data sources. Our DAS data source can be found in the central public DAS service repository, , or at . PMID:19534743

  8. Annotation extension through protein family annotation coherence metrics

    PubMed Central

    Bastos, Hugo P.; Clarke, Luka A.; Couto, Francisco M.

    2013-01-01

    Protein functional annotation consists in associating proteins with textual descriptors elucidating their biological roles. The bulk of annotation is done via automated procedures that ultimately rely on annotation transfer. Despite a large number of existing protein annotation procedures the ever growing protein space is never completely annotated. One of the facets of annotation incompleteness derives from annotation uncertainty. Often when protein function cannot be predicted with enough specificity it is instead conservatively annotated with more generic terms. In a scenario of protein families or functionally related (or even dissimilar) sets this leads to a more difficult task of using annotations to compare the extent of functional relatedness among all family or set members. However, we postulate that identifying sub-sets of functionally coherent proteins annotated at a very specific level, can help the annotation extension of other incompletely annotated proteins within the same family or functionally related set. As an example we analyse the status of annotation of a set of CAZy families belonging to the Polysaccharide Lyase class. We show that through the use of visualization methods and semantic similarity based metrics it is possible to identify families and respective annotation terms within them that are suitable for possible annotation extension. Based on our analysis we then propose a semi-automatic methodology leading to the extension of single annotation terms within these partially annotated protein sets or families. PMID:24130572

  9. Benchmark study of automatic annotation of MALDI-TOF N-glycan profiles.

    PubMed

    Brito, Alejandro E; Kletter, Doron; Singhal, Mudita; Bern, Marshall

    2015-11-01

    Human experts can annotate peaks in MALDI-TOF profiles of detached N-glycans with some degree of accuracy. Even though MALDI-TOF profiles give only intact masses without any fragmentation information, expert knowledge of the most common glycans and biosynthetic pathways in the biological system can point to a small set of most likely glycan structures at the "cartoon" level of detail. Cartoonist is a recently developed, fully automatic annotation tool for MALDI-TOF glycan profiles. Here we benchmark Cartoonist's automatic annotations against human expert annotations on human and mouse N-glycan data from the Consortium for Functional Glycomics. We find that Cartoonist and expert annotations largely agree, but the expert tends to annotate more specifically, meaning fewer suggested structures per peak, and Cartoonist more comprehensively, meaning more annotated peaks. On peaks for which both Cartoonist and the expert give unique cartoons, the two cartoons agree in over 90% of all cases. This article is part of a Special Issue entitled: Computational Proteomics. PMID:26047718

  10. ParsEval: parallel comparison and analysis of gene structure annotations

    PubMed Central

    2012-01-01

    Background Accurate gene structure annotation is a fundamental but somewhat elusive goal of genome projects, as witnessed by the fact that (model) genomes typically undergo several cycles of re-annotation. In many cases, it is not only different versions of annotations that need to be compared but also different sources of annotation of the same genome, derived from distinct gene prediction workflows. Such comparisons are of interest to annotation providers, prediction software developers, and end-users, who all need to assess what is common and what is different among distinct annotation sources. We developed ParsEval, a software application for pairwise comparison of sets of gene structure annotations. ParsEval calculates several statistics that highlight the similarities and differences between the two sets of annotations provided. These statistics are presented in an aggregate summary report, with additional details provided as individual reports specific to non-overlapping, gene-model-centric genomic loci. Genome browser styled graphics embedded in these reports help visualize the genomic context of the annotations. Output from ParsEval is both easily read and parsed, enabling systematic identification of problematic gene models for subsequent focused analysis. Results ParsEval is capable of analyzing annotations for large eukaryotic genomes on typical desktop or laptop hardware. In comparison to existing methods, ParsEval exhibits a considerable performance improvement, both in terms of runtime and memory consumption. Reports from ParsEval can provide relevant biological insights into the gene structure annotations being compared. Conclusions Implemented in C, ParsEval provides the quickest and most feature-rich solution for genome annotation comparison to date. The source code is freely available (under an ISC license) at http://parseval.sourceforge.net/. PMID:22852583

  11. Structural and functional annotation of the porcine immunome

    PubMed Central

    2013-01-01

    Background The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine performance, yet the structure and function of genes comprising the pig immunome are not well-characterized. The completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems. Results The Immune Response Annotation Group (IRAG) used computational curation and manual annotation of the swine genome assembly 10.2 (Sscrofa10.2) to refine the currently available automated annotation of 1,369 immunity-related genes through sequence-based comparison to genes in other species. Within these genes, we annotated 3,472 transcripts. Annotation provided evidence for gene expansions in several immune response families, and identified artiodactyl-specific expansions in the cathelicidin and type 1 Interferon families. We found gene duplications for 18 genes, including 13 immune response genes and five non-immune response genes discovered in the annotation process. Manual annotation provided evidence for many new alternative splice variants and 8 gene duplications. Over 1,100 transcripts without porcine sequence evidence were detected using cross-species annotation. We used a functional approach to discover and accurately annotate porcine immune response genes. A co-expression clustering analysis of transcriptomic data from selected experimental infections or immune stimulations of blood, macrophages or lymph nodes identified a large cluster of genes that exhibited a correlated positive response upon infection across multiple pathogens or immune stimuli. Interestingly, this gene cluster (cluster 4) is enriched for known general human immune response genes, yet contains many un-annotated porcine genes. A phylogenetic analysis of the encoded proteins of cluster 4 genes showed that 15% exhibited an accelerated

  12. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database.

    PubMed

    Kobayashi, Naohiro; Harano, Yoko; Tochio, Naoya; Nakatani, Eiichi; Kigawa, Takanori; Yokoyama, Shigeyuki; Mading, Steve; Ulrich, Eldon L; Markley, John L; Akutsu, Hideo; Fujiwara, Toshimichi

    2012-08-01

    Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including (1)H, (13)C and (15)N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001-2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies. PMID:22689068

  13. The Rice Annotation Project Database (RAP-DB): 2008 update.

    PubMed

    Tanaka, Tsuyoshi; Antonio, Baltazar A; Kikuchi, Shoshi; Matsumoto, Takashi; Nagamura, Yoshiaki; Numa, Hisataka; Sakai, Hiroaki; Wu, Jianzhong; Itoh, Takeshi; Sasaki, Takuji; Aono, Ryo; Fujii, Yasuyuki; Habara, Takuya; Harada, Erimi; Kanno, Masako; Kawahara, Yoshihiro; Kawashima, Hiroaki; Kubooka, Hiromi; Matsuya, Akihiro; Nakaoka, Hajime; Saichi, Naomi; Sanbonmatsu, Ryoko; Sato, Yoshiharu; Shinso, Yuji; Suzuki, Mami; Takeda, Jun-ichi; Tanino, Motohiko; Todokoro, Fusano; Yamaguchi, Kaori; Yamamoto, Naoyuki; Yamasaki, Chisato; Imanishi, Tadashi; Okido, Toshihisa; Tada, Masahito; Ikeo, Kazuho; Tateno, Yoshio; Gojobori, Takashi; Lin, Yao-Cheng; Wei, Fu-Jin; Hsing, Yue-ie; Zhao, Qiang; Han, Bin; Kramer, Melissa R; McCombie, Richard W; Lonsdale, David; O'Donovan, Claire C; Whitfield, Eleanor J; Apweiler, Rolf; Koyanagi, Kanako O; Khurana, Jitendra P; Raghuvanshi, Saurabh; Singh, Nagendra K; Tyagi, Akhilesh K; Haberer, Georg; Fujisawa, Masaki; Hosokawa, Satomi; Ito, Yukiyo; Ikawa, Hiroshi; Shibata, Michie; Yamamoto, Mayu; Bruskiewich, Richard M; Hoen, Douglas R; Bureau, Thomas E; Namiki, Nobukazu; Ohyanagi, Hajime; Sakai, Yasumichi; Nobushima, Satoshi; Sakata, Katsumi; Barrero, Roberto A; Sato, Yutaka; Souvorov, Alexandre; Smith-White, Brian; Tatusova, Tatiana; An, Suyoung; An, Gynheung; OOta, Satoshi; Fuks, Galina; Fuks, Galina; Messing, Joachim; Christie, Karen R; Lieberherr, Damien; Kim, HyeRan; Zuccolo, Andrea; Wing, Rod A; Nobuta, Kan; Green, Pamela J; Lu, Cheng; Meyers, Blake C; Chaparro, Cristian; Piegu, Benoit; Panaud, Olivier; Echeverria, Manuel

    2008-01-01

    The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/. PMID:18089549

  14. A Framework for Comparing Phenotype Annotations of Orthologous Genes

    PubMed Central

    Bodenreider, Olivier; Burgun, Anita

    2015-01-01

    Objectives Animal models are a key resource for the investigation of human diseases. In contrast to functional annotation, phenotype annotation is less standard, and comparing phenotypes across species remains challenging. The objective of this paper is to propose a framework for comparing phenotype annotations of orthologous genes based on the Medical Subject Headings (MeSH) indexing of biomedical articles in which these genes are discussed. Methods 17,769 pairs of orthologous genes (mouse and human) are downloaded from the Mouse Genome Informatics (MGI) system and linked to biomedical articles through Entrez Gene. MeSH index terms corresponding to diseases are extracted from Medline. Results 11,111 pairs of genes exhibited at least one phenotype annotation for each gene in the pair. Among these, 81% have at least one phenotype annotation in common, 80% have at least one annotation specific to the human gene and 84% have at least one annotation specific to the mouse gene. Four disease categories represent 54% of all phenotype annotations. Conclusions This framework supports the curation of phenotype annotation and the generation of research hypotheses based on comparative studies. PMID:20841896

  15. Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential.

    PubMed

    Biswas, Manosh Kumar; Liu, Yuxuan; Li, Chunyu; Sheng, Ou; Mayer, Christoph; Yi, Ganjun

    2015-01-01

    The development of organized, informative, robust, user-friendly, and freely accessible molecular markers is imperative to the Musa marker assisted breeding program. Although several hundred SSR markers have already been developed, the number of informative, robust, and freely accessible Musa markers remains inadequate for some breeding applications. In view of this issue, we surveyed SSRs in four different data sets, developed large-scale non-redundant highly informative therapeutic SSR markers, and classified them according to their attributes, as well as analyzed their cross-taxon transferability and utility for the genetic study of Musa and its relatives. A high SSR frequency (177 per Mbp) was found in the Musa genome. AT-rich dinucleotide repeats are predominant, and trinucleotide repeats are the most abundant in transcribed regions. A significant number of Musa SSRs are associated with pre-miRNAs, and 83% of these SSRs are promising candidates for the development of therapeutic SSR markers. Overall, 74% of the SSR markers were polymorphic, and 94% were transferable to at least one Musa spp. Two hundred forty-three markers generated a total of 1047 alleles, with 2-8 alleles each and an average of 4.38 alleles per locus. The PIC values ranged from 0.31 to 0.89 and averaged 0.71. We report the largest set of non-redundant, polymorphic, new SSR markers to be developed in Musa. These additional markers could be a valuable resource for marker-assisted breeding, genetic diversity and genomic studies of Musa and related species. PMID:26121637

  16. An annotated energy bibliography

    NASA Technical Reports Server (NTRS)

    Blow, S. J.

    1979-01-01

    Comprehensive annotated compilation of books, journals, periodicals, and reports on energy and energy related topics, contains approximately 10,0000 tehcnical and nontechnical references from bibliographic and other sources dated January 1975 through May 1977.

  17. Semantic Annotation of Mutable Data

    PubMed Central

    Morris, Robert A.; Dou, Lei; Hanken, James; Kelly, Maureen; Lowery, David B.; Ludäscher, Bertram; Macklin, James A.; Morris, Paul J.

    2013-01-01

    Electronic annotation of scientific data is very similar to annotation of documents. Both types of annotation amplify the original object, add related knowledge to it, and dispute or support assertions in it. In each case, annotation is a framework for discourse about the original object, and, in each case, an annotation needs to clearly identify its scope and its own terminology. However, electronic annotation of data differs from annotation of documents: the content of the annotations, including expectations and supporting evidence, is more often shared among members of networks. Any consequent actions taken by the holders of the annotated data could be shared as well. But even those current annotation systems that admit data as their subject often make it difficult or impossible to annotate at fine-enough granularity to use the results in this way for data quality control. We address these kinds of issues by offering simple extensions to an existing annotation ontology and describe how the results support an interest-based distribution of annotations. We are using the result to design and deploy a platform that supports annotation services overlaid on networks of distributed data, with particular application to data quality control. Our initial instance supports a set of natural science collection metadata services. An important application is the support for data quality control and provision of missing data. A previous proof of concept demonstrated such use based on data annotations modeled with XML-Schema. PMID:24223697

  18. Building a genome database using an object-oriented approach.

    PubMed

    Barbasiewicz, Anna; Liu, Lin; Lang, B Franz; Burger, Gertraud

    2002-01-01

    GOBASE is a relational database that integrates data associated with mitochondria and chloroplasts. The most important data in GOBASE, i. e., molecular sequences and taxonomic information, are obtained from the public sequence data repository at the National Center for Biotechnology Information (NCBI), and are validated by our experts. Maintaining a curated genomic database comes with a towering labor cost, due to the shear volume of available genomic sequences and the plethora of annotation errors and omissions in records retrieved from public repositories. Here we describe our approach to increase automation of the database population process, thereby reducing manual intervention. As a first step, we used Unified Modeling Language (UML) to construct a list of potential errors. Each case was evaluated independently, and an expert solution was devised, and represented as a diagram. Subsequently, the UML diagrams were used as templates for writing object-oriented automation programs in the Java programming language. PMID:12542407

  19. Genome-wide annotation and characterization of CLAVATA/ESR (CLE) peptide hormones of soybean (Glycine max) and common bean (Phaseolus vulgaris), and their orthologues of Arabidopsis thaliana

    PubMed Central

    Hastwell, April H.; Gresshoff, Peter M.; Ferguson, Brett J.

    2015-01-01

    CLE peptides are key regulators of cell proliferation and differentiation in plant shoots, roots, vasculature, and legume nodules. They are C-terminally encoded peptides that are post-translationally cleaved and modified from their corresponding pre-propeptides to produce a final ligand that is 12–13 amino acids in length. In this study, an array of bionformatic and comparative genomic approaches was used to identify and characterize the complete family of CLE peptide-encoding genes in two of the world’s most important crop species, soybean and common bean. In total, there are 84 CLE peptide-encoding genes in soybean (considerably more than the 32 present in Arabidopsis), including three pseudogenes and two multi-CLE domain genes having six putative CLE domains each. In addition, 44 CLE peptide-encoding genes were identified in common bean. In silico characterization was used to establish all soybean homeologous pairs, and to identify corresponding gene orthologues present in common bean and Arabidopsis. The soybean CLE pre-propeptide family was further analysed and separated into seven distinct groups based on structure, with groupings strongly associated with the CLE domain sequence and function. These groups provide evolutionary insight into the CLE peptide families of soybean, common bean, and Arabidopsis, and represent a novel tool that can aid in the functional characterization of the peptides. Transcriptional evidence was also used to provide further insight into the location and function of all CLE peptide-encoding members currently available in gene atlases for the three species. Taken together, this in-depth analysis helped to identify and categorize the complete CLE peptide families of soybean and common bean, established gene orthologues within the two legume species, and Arabidopsis, and provided a platform to help compare, contrast, and identify the function of critical CLE peptide hormones in plant development. PMID:26188205

  20. UCSC Data Integrator and Variant Annotation Integrator

    PubMed Central

    Hinrichs, Angie S.; Raney, Brian J.; Speir, Matthew L.; Rhead, Brooke; Casper, Jonathan; Karolchik, Donna; Kuhn, Robert M.; Rosenbloom, Kate R.; Zweig, Ann S.; Haussler, David; Kent, W. James

    2016-01-01

    Summary: Two new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user's own custom track data and/or data from track hubs. The Data Integrator combines columns from multiple data tracks, showing all items from the first track along with overlapping items from the other tracks. The Variant Annotation Integrator is tailored to adding functional annotations to variant calls; it offers a more restricted set of underlying data tracks but adds predictions of each variant's consequences for any overlapping or nearby gene transcript. When available, it optionally adds additional annotations including effect prediction scores from dbNSFP for missense mutations, ENCODE regulatory summary tracks and conservation scores. Availability and implementation: The web tools are freely available at http://genome.ucsc.edu/ and the underlying database is available for download at http://hgdownload.cse.ucsc.edu/. The software (written in C and Javascript) is available from https://genome-store.ucsc.edu/ and is freely available for academic and non-profit usage; commercial users must obtain a license. Contact: angie@soe.ucsc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26740527

  1. Comparative validation of the D. melanogaster modENCODE transcriptome annotation

    PubMed Central

    Chen, Zhen-Xia; Sturgill, David; Qu, Jiaxin; Jiang, Huaiyang; Park, Soo; Boley, Nathan; Suzuki, Ana Maria; Fletcher, Anthony R.; Plachetzki, David C.; FitzGerald, Peter C.; Artieri, Carlo G.; Atallah, Joel; Barmina, Olga; Brown, James B.; Blankenburg, Kerstin P.; Clough, Emily; Dasgupta, Abhijit; Gubbala, Sai; Han, Yi; Jayaseelan, Joy C.; Kalra, Divya; Kim, Yoo-Ah; Kovar, Christie L.; Lee, Sandra L.; Li, Mingmei; Malley, James D.; Malone, John H.; Mathew, Tittu; Mattiuzzo, Nicolas R.; Munidasa, Mala; Muzny, Donna M.; Ongeri, Fiona; Perales, Lora; Przytycka, Teresa M.; Pu, Ling-Ling; Robinson, Garrett; Thornton, Rebecca L.; Saada, Nehad; Scherer, Steven E.; Smith, Harold E.; Vinson, Charles; Warner, Crystal B.; Worley, Kim C.; Wu, Yuan-Qing; Zou, Xiaoyan; Cherbas, Peter; Kellis, Manolis; Eisen, Michael B.; Piano, Fabio; Kionte, Karin; Fitch, David H.; Sternberg, Paul W.; Cutter, Asher D.; Duff, Michael O.; Hoskins, Roger A.; Graveley, Brenton R.; Gibbs, Richard A.; Bickel, Peter J.; Kopp, Artyom; Carninci, Piero; Celniker, Susan E.; Oliver, Brian; Richards, Stephen

    2014-01-01

    Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community. PMID:24985915

  2. Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

    PubMed

    Chen, Zhen-Xia; Sturgill, David; Qu, Jiaxin; Jiang, Huaiyang; Park, Soo; Boley, Nathan; Suzuki, Ana Maria; Fletcher, Anthony R; Plachetzki, David C; FitzGerald, Peter C; Artieri, Carlo G; Atallah, Joel; Barmina, Olga; Brown, James B; Blankenburg, Kerstin P; Clough, Emily; Dasgupta, Abhijit; Gubbala, Sai; Han, Yi; Jayaseelan, Joy C; Kalra, Divya; Kim, Yoo-Ah; Kovar, Christie L; Lee, Sandra L; Li, Mingmei; Malley, James D; Malone, John H; Mathew, Tittu; Mattiuzzo, Nicolas R; Munidasa, Mala; Muzny, Donna M; Ongeri, Fiona; Perales, Lora; Przytycka, Teresa M; Pu, Ling-Ling; Robinson, Garrett; Thornton, Rebecca L; Saada, Nehad; Scherer, Steven E; Smith, Harold E; Vinson, Charles; Warner, Crystal B; Worley, Kim C; Wu, Yuan-Qing; Zou, Xiaoyan; Cherbas, Peter; Kellis, Manolis; Eisen, Michael B; Piano, Fabio; Kionte, Karin; Fitch, David H; Sternberg, Paul W; Cutter, Asher D; Duff, Michael O; Hoskins, Roger A; Graveley, Brenton R; Gibbs, Richard A; Bickel, Peter J; Kopp, Artyom; Carninci, Piero; Celniker, Susan E; Oliver, Brian; Richards, Stephen

    2014-07-01

    Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community. PMID:24985915

  3. UCSC genome browser tutorial.

    PubMed

    Zweig, Ann S; Karolchik, Donna; Kuhn, Robert M; Haussler, David; Kent, W James

    2008-08-01

    The University of California Santa Cruz (UCSC) Genome Bioinformatics website consists of a suite of free, open-source, on-line tools that can be used to browse, analyze, and query genomic data. These tools are available to anyone who has an Internet browser and an interest in genomics. The website provides a quick and easy-to-use visual display of genomic data. It places annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information. Many of the annotation tracks are submitted by scientists worldwide; the others are computed by the UCSC Genome Bioinformatics group from publicly available sequence data. It also allows users to upload and display their own experimental results or annotation sets by creating a custom track. The suite of tools, downloadable data files, and links to documentation and other information can be found at http://genome.ucsc.edu/. PMID:18514479

  4. Agents and Data Mining in Bioinformatics: Joining Data Gathering and Automatic Annotation with Classification and Distributed Clustering

    NASA Astrophysics Data System (ADS)

    Bazzan, Ana L. C.

    Multiagent systems and data mining techniques are being frequently used in genome projects, especially regarding the annotation process (annotation pipeline). This paper discusses annotation-related problems where agent-based and/or distributed data mining has been successfully employed.

  5. pico-PLAZA, a genome database of microbial photosynthetic eukaryotes.

    PubMed

    Vandepoele, Klaas; Van Bel, Michiel; Richard, Guilhem; Van Landeghem, Sofie; Verhelst, Bram; Moreau, Hervé; Van de Peer, Yves; Grimsley, Nigel; Piganeau, Gwenael

    2013-08-01

    With the advent of next generation genome sequencing, the number of sequenced algal genomes and transcriptomes is rapidly growing. Although a few genome portals exist to browse individual genome sequences, exploring complete genome information from multiple species for the analysis of user-defined sequences or gene lists remains a major challenge. pico-PLAZA is a web-based resource (http://bioinformatics.psb.ugent.be/pico-plaza/) for algal genomics that combines different data types with intuitive tools to explore genomic diversity, perform integrative evolutionary sequence analysis and study gene functions. Apart from homologous gene families, multiple sequence alignments, phylogenetic trees, Gene Ontology, InterPro and text-mining functional annotations, different interactive viewers are available to study genome organization using gene collinearity and synteny information. Different search functions, documentation pages, export functions and an extensive glossary are available to guide non-expert scientists. To illustrate the versatility of the platform, different case studies are presented demonstrating how pico-PLAZA can be used to functionally characterize large-scale EST/RNA-Seq data sets and to perform environmental genomics. Functional enrichments analysis of 16 Phaeodactylum tricornutum transcriptome libraries offers a molecular view on diatom adaptation to different environments of ecological relevance. Furthermore, we show how complementary genomic data sources can easily be combined to identify marker genes to study the diversity and distribution of algal species, for example in metagenomes, or to quantify intraspecific diversity from environmental strains. PMID:23826978

  6. A Factor Graph Approach to Automated GO Annotation.

    PubMed

    Spetale, Flavio E; Tapia, Elizabeth; Krsticevic, Flavia; Roda, Fernando; Bulacio, Pilar

    2016-01-01

    As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum. PMID:26771463

  7. A Factor Graph Approach to Automated GO Annotation

    PubMed Central

    Spetale, Flavio E.; Tapia, Elizabeth; Krsticevic, Flavia; Roda, Fernando; Bulacio, Pilar

    2016-01-01

    As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum. PMID:26771463

  8. Effective function annotation through catalytic residue conservation.

    PubMed

    George, Richard A; Spriggs, Ruth V; Bartlett, Gail J; Gutteridge, Alex; MacArthur, Malcolm W; Porter, Craig T; Al-Lazikani, Bissan; Thornton, Janet M; Swindells, Mark B

    2005-08-30

    Because of the extreme impact of genome sequencing projects, protein sequences without accompanying experimental data now dominate public databases. Homology searches, by providing an opportunity to transfer functional information between related proteins, have become the de facto way to address this. Although a single, well annotated, close relationship will often facilitate sufficient annotation, this situation is not always the case, particularly if mutations are present in important functional residues. When only distant relationships are available, the transfer of function information is more tenuous, and the likelihood of encountering several well annotated proteins with different functions is increased. The consequence for a researcher is a range of candidate functions with little way of knowing which, if any, are correct. Here, we address the problem directly by introducing a computational approach to accurately identify and segregate related proteins into those with a functional similarity and those where function differs. This approach should find a wide range of applications, including the interpretation of genomics/proteomics data and the prioritization of targets for high-throughput structure determination. The method is generic, but here we concentrate on enzymes and apply high-quality catalytic site data. In addition to providing a series of comprehensive benchmarks to show the overall performance of our approach, we illustrate its utility with specific examples that include the correct identification of haptoglobin as a nonenzymatic relative of trypsin, discrimination of acid-d-amino acid ligases from a much larger ligase pool, and the successful annotation of BioH, a structural genomics target. PMID:16037208

  9. ProteoAnnotator--open source proteogenomics annotation software supporting PSI standards.

    PubMed

    Ghali, Fawaz; Krishna, Ritesh; Perkins, Simon; Collins, Andrew; Xia, Dong; Wastling, Jonathan; Jones, Andrew R

    2014-12-01

    The recent massive increase in capability for sequencing genomes is producing enormous advances in our understanding of biological systems. However, there is a bottleneck in genome annotation--determining the structure of all transcribed genes. Experimental data from MS studies can play a major role in confirming and correcting gene structure--proteogenomics. However, there are some technical and practical challenges to overcome, since proteogenomics requires pipelines comprising a complex set of interconnected modules as well as bespoke routines, for example in protein inference and statistics. We are introducing a complete, open source pipeline for proteogenomics, called ProteoAnnotator, which incorporates a graphical user interface and implements the Proteomics Standards Initiative mzIdentML standard for each analysis stage. All steps are included as standalone modules with the mzIdentML library, allowing other groups to re-use the whole pipeline or constituent parts within other tools. We have developed new modules for pre-processing and combining multiple search databases, for performing peptide-level statistics on mzIdentML files, for scoring grouped protein identifications matched to a given genomic locus to validate that updates to the official gene models are statistically sound and for mapping end results back onto the genome. ProteoAnnotator is available from http://www.proteoannotator.org/. All MS data have been deposited in the ProteomeXchange with identifiers PXD001042 and PXD001390 (http://proteomecentral.proteomexchange.org/dataset/PXD001042; http://proteomecentral.proteomexchange.org/dataset/PXD001390). PMID:25297486

  10. A Novel Quality Measure and Correction Procedure for the Annotation of Microbial Translation Initiation Sites

    PubMed Central

    Overmars, Lex; Siezen, Roland J.; Francke, Christof

    2015-01-01

    The identification of translation initiation sites (TISs) constitutes an important aspect of sequence-based genome analysis. An erroneous TIS annotation can impair the identification of regulatory elements and N-terminal signal peptides, and also may flaw the determination of descent, for any particular gene. We have formulated a reference-free method to score the TIS annotation quality. The method is based on a comparison of the observed and expected distribution of all TISs in a particular genome given prior gene-calling. We have assessed the TIS annotations for all available NCBI RefSeq microbial genomes and found that approximately 87% is of appropriate quality, whereas 13% needs substantial improvement. We have analyzed a number of factors that could affect TIS annotation quality such as GC-content, taxonomy, the fraction of genes with a Shine-Dalgarno sequence and the year of publication. The analysis showed that only the first factor has a clear effect. We have then formulated a straightforward Principle Component Analysis-based TIS identification strategy to self-organize and score potential TISs. The strategy is independent of reference data and a priori calculations. A representative set of 277 genomes was subjected to the analysis and we found a clear increase in TIS annotation quality for the genomes with a low quality score. The PCA-based annotation was also compared with annotation with the current tool of reference, Prodigal. The comparison for the model genome of Escherichia coli K12 showed that both methods supplement each other and that prediction agreement can be used as an indicator of a correct TIS annotation. Importantly, the data suggest that the addition of a PCA-based strategy to a Prodigal prediction can be used to ‘flag’ TIS annotations for re-evaluation and in addition can be used to evaluate a given annotation in case a Prodigal annotation is lacking. PMID:26204119

  11. GIFtS: annotation landscape analysis with GeneCards

    PubMed Central

    Harel, Arye; Inger, Aron; Stelzer, Gil; Strichman-Almashanu, Liora; Dalah, Irina; Safran, Marilyn; Lancet, Doron

    2009-01-01

    Background Gene annotation is a pivotal component in computational genomics, encompassing prediction of gene function, expression analysis, and sequence scrutiny. Hence, quantitative measures of the annotation landscape constitute a pertinent bioinformatics tool. GeneCards® is a gene-centric compendium of rich annotative information for over 50,000 human gene entries, building upon 68 data sources, including Gene Ontology (GO), pathways, interactions, phenotypes, publications and many more. Results We present the GeneCards Inferred Functionality Score (GIFtS) which allows a quantitative assessment of a gene's annotation status, by exploiting the unique wealth and diversity of GeneCards information. The GIFtS tool, linked from the GeneCards home page, facilitates browsing the human genome by searching for the annotation level of a specified gene, retrieving a list of genes within a specified range of GIFtS value, obtaining random genes with a specific GIFtS value, and experimenting with the GIFtS weighting algorithm for a variety of annotation categories. The bimodal shape of the GIFtS distribution suggests a division of the human gene repertoire into two main groups: the high-GIFtS peak consists almost entirely of protein-coding genes; the low-GIFtS peak consists of genes from all of the categories. Cluster analysis of GIFtS annotation vectors provides the classification of gene groups by detailed positioning in the annotation arena. GIFtS also provide measures which enable the evaluation of the databases that serve as GeneCards sources. An inverse correlation is found (for GIFtS>25) between the number of genes annotated by each source, and the average GIFtS value of genes associated with that source. Three typical source prototypes are revealed by their GIFtS distribution: genome-wide sources, sources comprising mainly highly annotated genes, and sources comprising mainly poorly annotated genes. The degree of accumulated knowledge for a given gene measured by

  12. Annotation: The Savant Syndrome

    ERIC Educational Resources Information Center

    Heaton, Pamela; Wallace, Gregory L.

    2004-01-01

    Background: Whilst interest has focused on the origin and nature of the savant syndrome for over a century, it is only within the past two decades that empirical group studies have been carried out. Methods: The following annotation briefly reviews relevant research and also attempts to address outstanding issues in this research area.…

  13. Collaborative Movie Annotation

    NASA Astrophysics Data System (ADS)

    Zad, Damon Daylamani; Agius, Harry

    In this paper, we focus on metadata for self-created movies like those found on YouTube and Google Video, the duration of which are increasing in line with falling upload restrictions. While simple tags may have been sufficient for most purposes for traditionally very short video footage that contains a relatively small amount of semantic content, this is not the case for movies of longer duration which embody more intricate semantics. Creating metadata is a time-consuming process that takes a great deal of individual effort; however, this effort can be greatly reduced by harnessing the power of Web 2.0 communities to create, update and maintain it. Consequently, we consider the annotation of movies within Web 2.0 environments, such that users create and share that metadata collaboratively and propose an architecture for collaborative movie annotation. This architecture arises from the results of an empirical experiment where metadata creation tools, YouTube and an MPEG-7 modelling tool, were used by users to create movie metadata. The next section discusses related work in the areas of collaborative retrieval and tagging. Then, we describe the experiments that were undertaken on a sample of 50 users. Next, the results are presented which provide some insight into how users interact with existing tools and systems for annotating movies. Based on these results, the paper then develops an architecture for collaborative movie annotation.

  14. Annotated Bibliography. First Edition.

    ERIC Educational Resources Information Center

    Haring, Norris G.

    An annotated bibliography which presents approximately 300 references from 1951 to 1973 on the education of severely/profoundly handicapped persons. Citations are grouped alphabetically by author's name within the following categories: characteristics and treatment, gross motor development, sensory and motor development, physical therapy for the…

  15. Ghostwriting: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Simmons, Donald B.

    Drawn from communication journals, historical and news magazines, business and industrial magazines, political science and world affairs journals, general interest periodicals, and literary and political review magazines, the approximately 90 entries in this annotated bibliography discuss ghostwriting as practiced through the ages and reveal the…

  16. Protein function annotation using protein domain family resources.

    PubMed

    Das, Sayoni; Orengo, Christine A

    2016-01-15

    As a result of the genome sequencing and structural genomics initiatives, we have a wealth of protein sequence and structural data. However, only about 1% of these proteins have experimental functional annotations. As a result, computational approaches that can predict protein functions are essential in bridging this widening annotation gap. This article reviews the current approaches of protein function prediction using structure and sequence based classification of protein domain family resources with a special focus on functional families in the CATH-Gene3D resource. PMID:26434392

  17. Transcriptome annotation using tandem SAGE tags

    PubMed Central

    Rivals, Eric; Boureux, Anthony; Lejeune, Mireille; Ottones, Florence; Pecharromàn Pérez, Oscar; Tarhio, Jorma; Pierrat, Fabien; Ruffle, Florence; Commes, Thérèse; Marti, Jacques

    2007-01-01

    Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of gene expression (SAGE) can reveal new Poly(A) RNAs transcribed from previously unrecognized chromosomal regions. However, conventional SAGE tags are too short to identify unambiguously unique sites in large genomes. Here, we design a novel strategy with tags anchored on two different restrictions sites of cDNAs. New transcripts are then tentatively defined by the two SAGE tags in tandem and by the spanning sequence read on the genome between these tagged sites. Having developed a new algorithm to locate these tag-delimited genomic sequences (TDGS), we first validated its capacity to recognize known genes and its ability to reveal new transcripts with two SAGE libraries built in parallel from a single RNA sample. Our algorithm proves fast enough to experiment this strategy at a large scale. We then collected and processed the complete sets of human SAGE tags to predict yet unknown transcripts. A cross-validation with tiling arrays data shows that 47% of these TDGS overlap transcriptional active regions. Our method provides a new and complementary approach for complex transcriptome annotation. PMID:17709346

  18. Jannovar: a java library for exome annotation.

    PubMed

    Jäger, Marten; Wang, Kai; Bauer, Sebastian; Smedley, Damian; Krawitz, Peter; Robinson, Peter N

    2014-05-01

    Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects. Here, we present Jannovar, a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar can also perform family-based pedigree analysis with Variant Call Format (VCF) files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data. Jannovar is freely available under the BSD2 license. Source code as well as the Java application and library file can be downloaded from http://compbio.charite.de (with tutorial) and https://github.com/charite/jannovar. PMID:24677618

  19. RELATIONSHIP BETWEEN PHYLOGENETIC DISTRIBUTION AND GENOMIC FEATURES IN NEUROSPORA CRASSA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the post-genome era, insufficient functional annotation of predicted genes greatly restricts the potential of mining genome data. We demonstrate that an evolutionary approach, which is independent of functional annotation, has great potential as a tool for genome analysis. We chose the genome o...

  20. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    SciTech Connect

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R

    2007-12-10

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  1. PAVIS: a tool for Peak Annotation and Visualization.

    PubMed

    Huang, Weichun; Loganantharaj, Rasiah; Schroeder, Bryce; Fargo, David; Li, Leping

    2013-12-01

    We introduce a web-based tool, Peak Annotation and Visualization (PAVIS), for annotating and visualizing ChIP-seq peak data. PAVIS is designed with non-bioinformaticians in mind and presents a straightforward user interface to facilitate biological interpretation of ChIP-seq peak or other genomic enrichment data. PAVIS, through association with annotation, provides relevant genomic context for each peak, such as peak location relative to genomic features including transcription start site, intron, exon or 5'/3'-untranslated region. PAVIS reports the relative enrichment P-values of peaks in these functionally distinct categories, and provides a summary plot of the relative proportion of peaks in each category. PAVIS, unlike many other resources, provides a peak-oriented annotation and visualization system, allowing dynamic visualization of tens to hundreds of loci from one or more ChIP-seq experiments, simultaneously. PAVIS enables rapid, and easy examination and cross-comparison of the genomic context and potential functions of the underlying genomic elements, thus supporting downstream hypothesis generation. PMID:24008416

  2. Enhanced Acylcarnitine Annotation in High-Resolution Mass Spectrometry Data: Fragmentation Analysis for the Classification and Annotation of Acylcarnitines

    PubMed Central

    van der Hooft, Justin J. J.; Ridder, Lars; Barrett, Michael P.; Burgess, Karl E. V.

    2015-01-01

    Metabolite annotation and identification are primary challenges in untargeted metabolomics experiments. Rigorous workflows for reliable annotation of mass features with chemical structures or compound classes are needed to enhance the power of untargeted mass spectrometry. High-resolution mass spectrometry considerably improves the confidence in assigning elemental formulas to mass features in comparison to nominal mass spectrometry, and embedding of fragmentation methods enables more reliable metabolite annotations and facilitates metabolite classification. However, the analysis of mass fragmentation spectra can be a time-consuming step and requires expert knowledge. This study demonstrates how characteristic fragmentations, specific to compound classes, can be used to systematically analyze their presence in complex biological extracts like urine that have undergone untargeted mass spectrometry combined with data dependent or targeted fragmentation. Human urine extracts were analyzed using normal phase liquid chromatography (hydrophilic interaction chromatography) coupled to an Ion Trap-Orbitrap hybrid instrument. Subsequently, mass chromatograms and collision-induced dissociation and higher-energy collisional dissociation (HCD) fragments were annotated using the freely available MAGMa software1. Acylcarnitines play a central role in energy metabolism by transporting fatty acids into the mitochondrial matrix. By filtering on a combination of a mass fragment and neutral loss designed based on the MAGMa fragment annotations, we were able to classify and annotate 50 acylcarnitines in human urine extracts, based on high-resolution mass spectrometry HCD fragmentation spectra at different energies for all of them. Of these annotated acylcarnitines, 31 are not described in HMDB yet and for only 4 annotated acylcarnitines the fragmentation spectra could be matched to reference spectra. Therefore, we conclude that the use of mass fragmentation filters within the context

  3. Considerations to improve functional annotations in biological databases.

    PubMed

    Benítez-Páez, Alfonso

    2009-12-01

    Despite the great effort to design efficient systems allowing the electronic indexation of information concerning genes, proteins, structures, and interactions published daily in scientific journals, some problems are still observed in specific tasks such as functional annotation. The annotation of function is a critical issue for bioinformatic routines, such as for instance, in functional genomics and the further prediction of unknown protein function, which are highly dependent of the quality of existing annotations. Some information management systems evolve to efficiently incorporate information from large-scale projects, but often, annotation of single records from the literature is difficult and slow. In this short report, functional characterizations of a representative sample of the entire set of uncharacterized proteins from Escherichia coli K12 was compiled from Swiss-Prot, PubMed, and EcoCyc and demonstrate a functional annotation deficit in biological databases. Some issues are postulated as causes of the lack of annotation, and different solutions are evaluated and proposed to avoid them. The hope is that as a consequence of these observations, there will be new impetus to improve the speed and quality of functional annotation and ultimately provide updated, reliable information to the scientific community. PMID:20050264

  4. An Ontology-Based GIS for Genomic Data Management of Rumen Microbes

    PubMed Central

    Jelokhani-Niaraki, Saber; Minuchehr, Zarrin; Nassiri, Mohammad Reza

    2015-01-01

    During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data. PMID:25873847

  5. An Ontology-Based GIS for Genomic Data Management of Rumen Microbes.

    PubMed

    Jelokhani-Niaraki, Saber; Tahmoorespur, Mojtaba; Minuchehr, Zarrin; Nassiri, Mohammad Reza

    2015-03-01

    During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data. PMID:25873847

  6. Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data

    PubMed Central

    Rawat, Vimal; Abdelsamad, Ahmed; Pietzenuk, Björn; Seymour, Danelle K.; Koenig, Daniel; Weigel, Detlef; Pecinka, Ales; Schneeberger, Korbinian

    2015-01-01

    Gene model annotations are important community resources that ensure comparability and reproducibility of analyses and are typically the first step for functional annotation of genomic regions. Without up-to-date genome annotations, genome sequences cannot be used to maximum advantage. It is therefore essential to regularly update gene annotations by integrating the latest information to guarantee that reference annotations can remain a common basis for various types of analyses. Here, we report an improvement of the Arabidopsis lyrata gene annotation using extensive RNA-seq data. This new annotation consists of 31,132 protein coding gene models in addition to 2,089 genes with high similarity to transposable elements. Overall, ~87% of the gene models are corroborated by evidence of expression and 2,235 of these models feature multiple transcripts. Our updated gene annotation corrects hundreds of incorrectly split or merged gene models in the original annotation, and as a result the identification of alternative splicing events and differential isoform usage are vastly improved. PMID:26382944

  7. Detection of gene annotations and protein-protein interaction associated disorders through transitive relationships between integrated annotations

    PubMed Central

    2015-01-01

    Background Increasingly high amounts of heterogeneous and valuable controlled biomolecular annotations are available, but far from exhaustive and scattered in many databases. Several annotation integration and prediction approaches have been proposed, but these issues are still unsolved. We previously created a Genomic and Proteomic Knowledge Base (GPKB) that efficiently integrates many distributed biomolecular annotation and interaction data of several organisms, including 32,956,102 gene annotations, 273,522,470 protein annotations and 277,095 protein-protein interactions (PPIs). Results By comprehensively leveraging transitive relationships defined by the numerous association data integrated in GPKB, we developed a software procedure that effectively detects and supplement consistent biomolecular annotations not present in the integrated sources. According to some defined logic rules, it does so only when the semantic type of data and of their relationships, as well as the cardinality of the relationships, allow identifying molecular biology compliant annotations. Thanks to controlled consistency and quality enforced on data integrated in GPKB, and to the procedures used to avoid error propagation during their automatic processing, we could reliably identify many annotations, which we integrated in GPKB. They comprise 3,144 gene to pathway and 21,942 gene to biological function annotations of many organisms, and 1,027 candidate associations between 317 genetic disorders and 782 human PPIs. Overall estimated recall and precision of our approach were 90.56 % and 96.61 %, respectively. Co-functional evaluation of genes with known function showed high functional similarity between genes with new detected and known annotation to the same pathway; considering also the new detected gene functional annotations enhanced such functional similarity, which resembled the one existing between genes known to be annotated to the same pathway. Strong evidence was also found in

  8. FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation

    DOE PAGESBeta

    Bolleman, Jerven T.; Mungall, Christopher J.; Strozzi, Francesco; Baran, Joachim; Dumontier, Michel; Bonnal, Raoul J. P.; Buels, Robert; Hoehndorf, Robert; Fujisawa, Takatomo; Katayama, Toshiaki; et al

    2016-06-13

    In this study, nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. Here, we have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned “omics” areas. Using the same datamore » format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. In conclusion, our ontology allows users to uniformly describe – and potentially merge – sequence annotations from multiple sources. Data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.« less

  9. FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

    DOE PAGESBeta

    Bolleman, Jerven T.; Mungall, Christopher J.; Strozzi, Francesco; Baran, Joachim; Dumontier, Michel; Bonnal, Raoul J. P.; Buels, Robert; Hoehndorf, Robert; Fujisawa, Takatomo; Katayama, Toshiaki; et al

    2016-06-13

    Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. In this paper, we have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned “omics” areas. Using the same data formatmore » to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. Our ontology allows users to uniformly describe – and potentially merge – sequence annotations from multiple sources. Finally, data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.« less

  10. Using Nonexperts for Annotating Pharmacokinetic Drug-Drug Interaction Mentions in Product Labeling: A Feasibility Study

    PubMed Central

    Ning, Yifan; Hernandez, Andres; Horn, John R; Jacobson, Rebecca; Boyce, Richard D

    2016-01-01

    Background Because vital details of potential pharmacokinetic drug-drug interactions are often described in free-text structured product labels, manual curation is a necessary but expensive step in the development of electronic drug-drug interaction information resources. The use of nonexperts to annotate potential drug-drug interaction (PDDI) mentions in drug product label annotation may be a means of lessening the burden of manual curation. Objective Our goal was to explore the practicality of using nonexpert participants to annotate drug-drug interaction descriptions from structured product labels. By presenting annotation tasks to both pharmacy experts and relatively naïve participants, we hoped to demonstrate the feasibility of using nonexpert annotators for drug-drug information annotation. We were also interested in exploring whether and to what extent natural language processing (NLP) preannotation helped improve task completion time, accuracy, and subjective satisfaction. Methods Two experts and 4 nonexperts were asked to annotate 208 structured product label sections under 4 conditions completed sequentially: (1) no NLP assistance, (2) preannotation of drug mentions, (3) preannotation of drug mentions and PDDIs, and (4) a repeat of the no-annotation condition. Results were evaluated within the 2 groups and relative to an existing gold standard. Participants were asked to provide reports on the time required to complete tasks and their perceptions of task difficulty. Results One of the experts and 3 of the nonexperts completed all tasks. Annotation results from the nonexpert group were relatively strong in every scenario and better than the performance of the NLP pipeline. The expert and 2 of the nonexperts were able to complete most tasks in less than 3 hours. Usability perceptions were generally positive (3.67 for expert, mean of 3.33 for nonexperts). Conclusions The results suggest that nonexpert annotation might be a feasible option for comprehensive

  11. AgBase: a functional genomics resource for agriculture

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many agricultural species and their pathogens have sequenced genomes and more are in progress. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural ...

  12. Complete genome sequence of an attenuated Sparfloxacin-resistant Streptococcus agalactiae strain 138spar

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complete genome of a sparfloxacin-resistant Streptococcus agalactiae vaccine strain 138spar is 1,838,126 bp in size. The genome has 1892 coding sequences and 82 RNAs. The annotation of the genome is added by the NCBI Prokaryotic Genome Annotation Pipeline. The publishing of this genome will allo...

  13. Functional Annotations of Paralogs: A Blessing and a Curse.

    PubMed

    Zallot, Rémi; Harrison, Katherine J; Kolaczkowski, Bryan; de Crécy-Lagard, Valérie

    2016-01-01

    Gene duplication followed by mutation is a classic mechanism of neofunctionalization, producing gene families with functional diversity. In some cases, a single point mutation is sufficient to change the substrate specificity and/or the chemistry performed by an enzyme, making it difficult to accurately separate enzymes with identical functions from homologs with different functions. Because sequence similarity is often used as a basis for assigning functional annotations to genes, non-isofunctional gene families pose a great challenge for genome annotation pipelines. Here we describe how integrating evolutionary and functional information such as genome context, phylogeny, metabolic reconstruction and signature motifs may be required to correctly annotate multifunctional families. These integrative analyses can also lead to the discovery of novel gene functions, as hints from specific subgroups can guide the functional characterization of other members of the family. We demonstrate how careful manual curation processes using comparative genomics can disambiguate subgroups within large multifunctional families and discover their functions. We present the COG0720 protein family as a case study. We also discuss strategies to automate this process to improve the accuracy of genome functional annotation pipelines. PMID:27618105

  14. BμG@Sbase—a microbial gene expression and comparative genomic database

    PubMed Central

    Witney, Adam A.; Waldron, Denise E.; Brooks, Lucy A.; Tyler, Richard H.; Withers, Michael; Stoker, Neil G.; Wren, Brendan W.; Butcher, Philip D.; Hinds, Jason

    2012-01-01

    The reducing cost of high-throughput functional genomic technologies is creating a deluge of high volume, complex data, placing the burden on bioinformatics resources and tool development. The Bacterial Microarray Group at St George's (BμG@S) has been at the forefront of bacterial microarray design and analysis for over a decade and while serving as a hub of a global network of microbial research groups has developed BμG@Sbase, a microbial gene expression and comparative genomic database. BμG@Sbase (http://bugs.sgul.ac.uk/bugsbase/) is a web-browsable, expertly curated, MIAME-compliant database that stores comprehensive experimental annotation and multiple raw and analysed data formats. Consistent annotation is enabled through a structured set of web forms, which guide the user through the process following a set of best practices and controlled vocabulary. The database currently contains 86 expertly curated publicly available data sets (with a further 124 not yet published) and full annotation information for 59 bacterial microarray designs. The data can be browsed and queried using an explorer-like interface; integrating intuitive tree diagrams to present complex experimental details clearly and concisely. Furthermore the modular design of the database will provide a robust platform for integrating other data types beyond microarrays into a more Systems analysis based future. PMID:21948792

  15. Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation.

    PubMed

    Poos, Kathrin; Smida, Jan; Nathrath, Michaela; Maugg, Doris; Baumhoer, Daniel; Neumann, Anna; Korsching, Eberhard

    2014-01-01

    Osteosarcoma (OS) is the most common primary bone cancer exhibiting high genomic instability. This genomic instability affects multiple genes and microRNAs to a varying extent depending on patient and tumor subtype. Massive research is ongoing to identify genes including their gene products and microRNAs that correlate with disease progression and might be used as biomarkers for OS. However, the genomic complexity hampers the identification of reliable biomarkers. Up to now, clinico-pathological factors are the key determinants to guide prognosis and therapeutic treatments. Each day, new studies about OS are published and complicate the acquisition of information to support biomarker discovery and therapeutic improvements. Thus, it is necessary to provide a structured and annotated view on the current OS knowledge that is quick and easily accessible to researchers of the field. Therefore, we developed a publicly available database and Web interface that serves as resource for OS-associated genes and microRNAs. Genes and microRNAs were collected using an automated dictionary-based gene recognition procedure followed by manual review and annotation by experts of the field. In total, 911 genes and 81 microRNAs related to 1331 PubMed abstracts were collected (last update: 29 October 2013). Users can evaluate genes and microRNAs according to their potential prognostic and therapeutic impact, the experimental procedures, the sample types, the biological contexts and microRNA target gene interactions. Additionally, a pathway enrichment analysis of the collected genes highlights different aspects of OS progression. OS requires pathways commonly deregulated in cancer but also features OS-specific alterations like deregulated osteoclast differentiation. To our knowledge, this is the first effort of an OS database containing manual reviewed and annotated up-to-date OS knowledge. It might be a useful resource especially for the bone tumor research community, as specific

  16. Integrative annotation of chromatin elements from ENCODE data

    PubMed Central

    Hoffman, Michael M.; Ernst, Jason; Wilder, Steven P.; Kundaje, Anshul; Harris, Robert S.; Libbrecht, Max; Giardine, Belinda; Ellenbogen, Paul M.; Bilmes, Jeffrey A.; Birney, Ewan; Hardison, Ross C.; Dunham, Ian; Kellis, Manolis; Noble, William Stafford

    2013-01-01

    The ENCODE Project has generated a wealth of experimental information mapping diverse chromatin properties in several human cell lines. Although each such data track is independently informative toward the annotation of regulatory elements, their interrelations contain much richer information for the systematic annotation of regulatory elements. To uncover these interrelations and to generate an interpretable summary of the massive datasets of the ENCODE Project, we apply unsupervised learning methodologies, converting dozens of chromatin datasets into discrete annotation maps of regulatory regions and other chromatin elements across the human genome. These methods rediscover and summarize diverse aspects of chromatin architecture, elucidate the interplay between chromatin activity and RNA transcription, and reveal that a large proportion of the genome lies in a quiescent state, even across multiple cell types. The resulting annotation of non-coding regulatory elements correlate strongly with mammalian evolutionary constraint, and provide an unbiased approach for evaluating metrics of evolutionary constraint in human. Lastly, we use the regulatory annotations to revisit previously uncharacterized disease-associated loci, resulting in focused, testable hypotheses through the lens of the chromatin landscape. PMID:23221638

  17. Widowed Persons Service: Selected Annotated Bibliography.

    ERIC Educational Resources Information Center

    Bressler, Dawn, Comp.; And Others

    This document presents an annotated bibliography of books and articles on topics relevant to widowhood. These annotations are included: (1) 21 annotations on the grief process; (2) 11 annotations on personal observations about widowhood; (3) 16 annotations on practical problems surrounding widowhood, including legal and financial problems and job…

  18. Speech spectrogram expert

    SciTech Connect

    Johannsen, J.; Macallister, J.; Michalek, T.; Ross, S.

    1983-01-01

    Various authors have pointed out that humans can become quite adept at deriving phonetic transcriptions from speech spectrograms (as good as 90percent accuracy at the phoneme level). The authors describe an expert system which attempts to simulate this performance. The speech spectrogram expert (spex) is actually a society made up of three experts: a 2-dimensional vision expert, an acoustic-phonetic expert, and a phonetics expert. The visual reasoning expert finds important visual features of the spectrogram. The acoustic-phonetic expert reasons about how visual features relates to phonemes, and about how phonemes change visually in different contexts. The phonetics expert reasons about allowable phoneme sequences and transformations, and deduces an english spelling for phoneme strings. The speech spectrogram expert is highly interactive, allowing users to investigate hypotheses and edit rules. 10 references.

  19. Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1

    SciTech Connect

    Kim, Wook; Silby, Mark W.; Purvine, Samuel O.; Nicoll, Julie S.; Hixson, Kim K.; Monroe, Matthew E.; Nicora, Carrie D.; Lipton, Mary S.; Levy, Stuart B.

    2009-12-24

    Genome sequences are annotated by computational prediction of coding sequences, followed by similarity searches such as BLAST, which provide a layer of (possible) functional information. While the existence of processes such as alternative splicing complicates matters for eukaryote genomes, the view of bacterial genomes as a linear series of closely spaced genes leads to the assumption that computational annotations which predict such arrangements completely describe the coding capacity of bacterial genomes. We undertook a proteomic study to identify proteins expressed by Pseudomonas fluorescens Pf0-1 from genes which were not predicted during the genome annotation. Mapping peptides to the Pf0-1 genome sequence identified sixteen non-annotated protein-coding regions, of which nine were antisense to predicted genes, six were intergenic, and one read in the same direction as an annotated gene but in a different frame. The expression of all but one of the newly discovered genes was verified by RT-PCR. Few clues as to the function of the new genes were gleaned from informatic analyses, but potential orthologues in other Pseudomonas genomes were identified for eight of the new genes. The 16 newly identified genes improve the quality of the Pf0-1 genome annotation, and the detection of antisense protein-coding genes indicates the under-appreciated complexity of bacterial genome organization.

  20. Optimizing high performance computing workflow for protein functional annotation.

    PubMed

    Stanberry, Larissa; Rekepalli, Bhanu; Liu, Yuan; Giblock, Paul; Higdon, Roger; Montague, Elizabeth; Broomall, William; Kolker, Natali; Kolker, Eugene

    2014-09-10

    Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the protein sequence universe is rapidly expanding. Newly sequenced bacterial genomes alone contain over 7.5 million proteins. The rate of data generation has far surpassed that of protein annotation. The volume of protein data makes manual curation infeasible, whereas a high compute cost limits the utility of existing automated approaches. In this work, we present an improved and optmized automated workflow to enable large-scale protein annotation. The workflow uses high performance computing architectures and a low complexity classification algorithm to assign proteins into existing clusters of orthologous groups of proteins. On the basis of the Position-Specific Iterative Basic Local Alignment Search Tool the algorithm ensures at least 80% specificity and sensitivity of the resulting classifications. The workflow utilizes highly scalable parallel applications for classification and sequence alignment. Using Extreme Science and Engineering Discovery Environment supercomputers, the workflow processed 1,200,000 newly sequenced bacterial proteins. With the rapid expansion of the protein sequence universe, the proposed workflow will enable scientists to annotate big genome data. PMID:25313296

  1. Communication and Gender: Annotated Bibliography

    ERIC Educational Resources Information Center

    Todd-Mancillas, William R.; Krug, Linda

    Focusing on the similarities and differences in men's and women's verbal and nonverbal communication behavior, this 33-item annotated bibliography presents a sample of articles appearing in speech communication publications on the subject. Categories of the annotated bibliography are books, sexism and sexual harassment in academia, theoretic…

  2. Drug Education: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Mathieson, Moira B.

    This bibliography consists of a total of 215 entries dealing with drug education, including curriculum guides, and drawn from documents in the ERIC system. There are two sections, the first containing 130 annotated citations of documents and journal articles, and the second containing 85 citations of journal articles without annotations, but with…

  3. Women in Communication: Annotated Bibliography.

    ERIC Educational Resources Information Center

    Mills, Carol A.

    This annotated bibliography is designed to survey the field of women in communication. The bibliography is centered on a specific context: who are and who were the women who worked in the communication field, and specifically, what were their writings like? The 56 annotations date from 1949 through 1990 and deal mostly with books (especially…

  4. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation

    SciTech Connect

    Gupta, Nitin; Tanner, Stephen; Jaitly, Navdeep; Adkins, Joshua N.; Lipton, Mary S.; Edwards, Robert; Romine, Margaret F.; Osterman, Andrei; Bafna, Vineet; Smith, Richard D.; Pevzner, Pavel A.

    2007-09-04

    While bacterial genome annotations have significantly improved in recent years, techniques for bacterial proteome annotation (including post-translational chemical modifications, signal peptides, proteolytic events, etc.) are still in their infancy. At the same time, the number of sequenced bacterial genomes is rising sharply, far outpacing our ability to validate the predicted genes, let alone annotate bacterial proteomes. In this study, we use tandem mass spectrometry (MS/MS) to annotate the proteome of Shewanella oneidensis MR-1, an important microbe for bioremediation. In particular, we provide the first comprehensive map of post-translational modifications in a bacterial genome, including a large number of chemical modifications, signal peptide cleavages and cleavage of N-terminal methionine residues. We also detect multiple genes that were missed or assigned incorrect start positions by gene prediction programs and suggest corrections to improve the gene annotation. This study demonstrates that complementing every genome sequencing project by an MS/MS project would significantly improve both genome and proteome annotations for a reasonable cost.

  5. Clinical genomics information management software linking cancer genome sequence and clinical decisions.

    PubMed

    Watt, Stuart; Jiao, Wei; Brown, Andrew M K; Petrocelli, Teresa; Tran, Ben; Zhang, Tong; McPherson, John D; Kamel-Reid, Suzanne; Bedard, Philippe L; Onetto, Nicole; Hudson, Thomas J; Dancey, Janet; Siu, Lillian L; Stein, Lincoln; Ferretti, Vincent

    2013-09-01

    Using sequencing information to guide clinical decision-making requires coordination of a diverse set of people and activities. In clinical genomics, the process typically includes sample acquisition, template preparation, genome data generation, analysis to identify and confirm variant alleles, interpretation of clinical significance, and reporting to clinicians. We describe a software application developed within a clinical genomics study, to support this entire process. The software application tracks patients, samples, genomic results, decisions and reports across the cohort, monitors progress and sends reminders, and works alongside an electronic data capture system for the trial's clinical and genomic data. It incorporates systems to read, store, analyze and consolidate sequencing results from multiple technologies, and provides a curated knowledge base of tumor mutation frequency (from the COSMIC database) annotated with clinical significance and drug sensitivity to generate reports for clinicians. By supporting the entire process, the application provides deep support for clinical decision making, enabling the generation of relevant guidance in reports for verification by an expert panel prior to forwarding to the treating physician. PMID:23603536

  6. Considering Transposable Element Diversification in De Novo Annotation Approaches

    PubMed Central

    Flutre, Timothée; Duprat, Elodie; Feuillet, Catherine; Quesneville, Hadi

    2011-01-01

    Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high-throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species. PMID:21304975

  7. Complete genome sequence of a virulent Streptococcus agalactiae strain 138P isolated from disease Nile tilapia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complete genome of a virulent Streptococcus agalactiae strain 138P is 1838701 bp in size, containing 1831 genes. The genome has 1593 coding sequences, 152 pseudo genes, 16 rRNAs, 69 tRNAs, and 1 non-coding RNA. The annotation of the genome is added by the NCBI Prokaryotic Genome Annotation Pipel...

  8. Incorporating Non-Coding Annotations into Rare Variant Analysis

    PubMed Central

    Richardson, Tom G.; Campbell, Colin; Timpson, Nicholas J; Gaunt, Tom R.

    2016-01-01

    Background The success of collapsing methods which investigate the combined effect of rare variants on complex traits has so far been limited. The manner in which variants within a gene are selected prior to analysis has a crucial impact on this success, which has resulted in ana