for sequencing genomes D. The Human Genome Project II. Comparative Genomics III. Proteomics Genomics Compiling the sequence = genome sequenced multiple times to ensure the sequence is accurate #12;10 D. The Human Genome Project International research ...

We present an analysis of 203 completed genomes in the Gene3D resource (including 17 eukaryotes), which demonstrates that the number of protein families is continually expanding over time and that singleton-sequences appear to be an intrinsic part of the genomes. A significant proportion of the proteomes can be assigned to fewer than 6000 ...

Accurate and comprehensive gene structure annotation in emerging and assembled genomes is fundamental to comparative, functional, and translational genomics. We plan to build the cyberinfrastructure necessary for defining and accessing the plant gene space. Our Plant Genetic Data Base (PlantGDB) r...

The goal of the GRAIL project has been to create a comprehensive analysis environment where a host of questions about genes and genome structure can be answered as quickly and accurately as possible. Constructing this system has entailed solving a number ...

BackgroundModern biomedical research depends on a complete and accurate proteome. With the widespread adoption of new sequencing technologies, genome sequences are generated at a near exponential rate, diminishing the time and effort that can be invested in genome annotation. The resulting gene set contains numerous errors in even the ...

Abstract. In the wake of the genome data flow, we need- more urgently than ever- accurate tools to predict protein structure. The problem of predicting protein structure from sequence remains fundamentally unsolved despite more than three decades of intensive research effort. However, the wealth of evolutionary ...

ABSTRACT: BACKGROUND: Switchgrass, a C4 species and a warm-season grass native to the prairies of North America, has been targeted for development into an herbaceous biomass fuel crop. Genetic improvement of switchgrass feedstock traits through marker-assisted breeding and biotechnology approaches calls for genomic tools development. Establishment of integrated physical and ...

BackgroundSwitchgrass, a C4 species and a warm-season grass native to the prairies of North America, has been targeted for development into an herbaceous biomass fuel crop. Genetic improvement of switchgrass feedstock traits through marker-assisted breeding and biotechnology approaches calls for genomic tools development. Establishment of integrated physical and genetic maps ...

Comprehensive identification of the acquired mutations that cause common cancers will require genomic analyses of large sets of tumor samples. Typically, the tissue material available from tumor specimens is limited, which creates a demand for accurate template amplification. We therefore evaluated whether phi29-mediated whole genome ...

A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Early ...

The thermoacidophiles Sulfolobus solfataricus P2 and S. acidocaldarius 98-3 are considered key model organisms representing a major phylum of the Crenarchaeota. Because maintaining current, accurate genome information is indispensable for modern biology, we have updated gene function annotation using the arCOGs database, plus other available functional, ...

BackgroundIn order to maintain genome information accurately and relevantly, original genome annotations need to be updated and evaluated regularly. Manual reannotation of genomes is important as it can significantly reduce the propagation of errors and consequently diminishes the time spent on mistaken research. ...

In the four decades since the discovery of the basic structure of the DNA double helix, researchers have been investigating the more dynamic tertiary structures that DNA assumes in the various forms of chromatin. The tertiary structure of DNA is important because it is directly related to the function of the ...

BackgroundPlastid genome sequence information is vital to several disciplines in plant biology, including phylogenetics and molecular biology. The past five years have witnessed a dramatic increase in the number of completely sequenced plastid genomes, fuelled largely by advances in conventional Sanger sequencing technology. Here we report a further ...

Faced with the determination of many completely sequenced genomes, computational biology is now faced with the challenge of interpreting the significance of these data sets. A multiplicity of data-related problems impedes this goal: Biological annotations associated with raw data are often not normalized, and the data themselves are often poorly interrelated and their ...

The study of genome rearrangement is much harder than the corresponding problems on DNA and protein sequences, because of the occurrences of numerous combinatorial structures. By explicitly exploring these combinatorial structures, the recently developed adequate subgraph theory shows that a family of these ...

BackgroundDespite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. It continues to be interesting to develop new ab initio algorithms which not only accurately ...

CnidBase,the Cnidarian Evolutionary Genomics Database,is a tool for investigating the evolutionary, developmental and ecological factors that affect gene expression and gene function in cnidarians. In turn, CnidBase will help to illuminate the role of specific genes in shaping cnidarian biodiversity in the present day and in the distant past. CnidBase highlights evolutionary ...

Conventional comparative genomic hybridization (CGH), high-resolution oligonucleotide, and BAC array CGH have modernized the field of cytogenetics to enable access to unbalanced genomic aberrations such as whole or partial chromosomal gains and losses. The basic principle of array CGH involves hybridizing differentially labeled proband/test (e.g., tumor) ...

genomics, computational tools, evolution, genomic structure Web Page: httpA Novel Approach for Comparative Genomics & Annotation Transfer Alban MANCHERON Raluca URICARU Eric is genome comparison good for?" Genome comparison is crucial for genome ...

Computational methods for gene identification in genomic sequences typically have two phases: coding region prediction and gene parsing. While there are many effective methods for predicting coding regions (exons), parsing the predicted exons into proper gene structures, to a large extent, remains an unsolved problem. This paper presents an algorithm for ...

BackgroundThe 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.ResultsWe report here a functionally annotated ...

BackgroundGenome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular methods for reconstructing phylogeny from genome rearrangements include GRAPPA and MGR. However ...

Ways & Means 259 Marrying structure and genomics Burkhard Rost Address: European Molecular Biology]). What about the relationship between structure determination and genomics, however? Tomorrow Structural the under- standing of life. Objectives Structure determination ...

Data management has been identified as a crucial issue in all large-scale experimental projects. In this type of project, many different persons manipulate multiple objects in different locations; thus, unless complete and accurate records are maintained, it is extremely difficult to understand exactly what has been done, when it was done, who did it, and what exact protocol ...

Your Gene structure Annotation Tool for Eukaryotes (yrGATE) provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate ...

Structural genomics (SG) programs have developed during the last decade many novel methodologies for faster and more accurate structure determination. These new tools and approaches led to the determination of thousands of protein structures. The generation of enormous amounts of experimental ...

As complete genomes accumulate and the generation of genomic biodiversity proceeds at an accelerating pace, the need to understand the interaction between sequence evolution and protein structure and function rises in prominence. The pattern and pace of substitutions in proteins can provide important clues to functional importance, ...

transporter ho- Figure 2 (a) The glutamate transporter homolog (1XFH) contains both disrupted transmembrane genomes encode large numbers of small-molecule transporters with 6 or (more often) 12 transmembrane transmembrane helices, as well as for small-molecule transporters. With the availability of more accurate

Comprehensive understanding of functional elements in the human genome will require thorough interrogation and comparison of individual human genomes and genomic structures. Such an endeavor will require improvements in the throughputs and costs of DNA sequencing. Next-generation sequencing platforms have ...

Rational drug design relies on the 3D structures of biological macromolecules, with a particular emphasis on proteins. The structural genomics-based high-throughput structure determination platforms established by the Protein Structure Initiative (PSI) of the National Institute of General ...

BackgroundTransposable elements are the most abundant components of all characterized genomes of higher eukaryotes. It has been documented that these elements not only contribute to the shaping and reshaping of their host genomes, but also play significant roles in regulating gene expression, altering gene function, and creating new genes. Thus, complete ...

Genome sequencing of closely related individuals has yielded valuable insights that link genome evolution to phenotypic variations. However, advancement in sequencing technology has also led to an escalation in the number of poor quality drafted genomes assembled based on reference genomes that can have highly ...

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 ...