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Sample records for multiple-sequence local alignment

  1. Mulan: Multiple-Sequence Local Alignment and Visualization for Studying Function and Evolution

    SciTech Connect

    Ovcharenko, I; Loots, G; Giardine, B; Hou, M; Ma, J; Hardison, R; Stubbs, L; Miller, W

    2004-07-14

    Multiple sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes and detecting functional regulatory elements. With a growing number of partly or fully sequenced vertebrate genomes, effective tools for performing multiple comparisons are required to accurately and efficiently assist biological discoveries. Here we introduce Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the tba multi-aligner program for rapid identification of local sequence conservation and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA. Local multiple alignments computed by Mulan ensure reliable representation of short-and large-scale genomic rearrangements in distant organisms. Mulan allows for interactive modification of critical conservation parameters to differentially predict conserved regions in comparisons of both closely and distantly related species. We illustrate the uses and applications of the Mulan tool through multi-species comparisons of the GATA3 gene locus and the identification of elements that are conserved differently in avians than in other genomes allowing speculation on the evolution of birds. Source code for the aligners and the aligner-evaluation software can be freely downloaded from http://bio.cse.psu.edu/.

  2. SNUFER: A software for localization and presentation of single nucleotide polymorphisms using a Clustal multiple sequence alignment output file

    PubMed Central

    Mansur, Marco A B; Cardozo, Giovana P; Santos, Elaine V; Marins, Mozart

    2008-01-01

    SNUFER is a software for the automatic localization and generation of tables used for the presentation of single nucleotide polymorphisms (SNPs). After input of a fasta file containing the sequences to be analyzed, a multiple sequence alignment is generated using ClustalW ran inside SNUFER. The ClustalW output file is then used to generate a table which displays the SNPs detected in the aligned sequences and their degree of similarity. This table can be exported to Microsoft Word, Microsoft Excel or as a single text file, permitting further editing for publication. The software was written using Delphi 7 for programming and FireBird 2.0 for sequence database management. It is freely available for noncommercial use and can be downloaded from http://www.heranza.com.br/bioinformatica2.htm. PMID:19238196

  3. Multiple Sequence Alignment Based on Chaotic PSO

    NASA Astrophysics Data System (ADS)

    Lei, Xiu-Juan; Sun, Jing-Jing; Ma, Qian-Zhi

    This paper introduces a new improved algorithm called chaotic PSO (CPSO) based on the thought of chaos optimization to solve multiple sequence alignment. For one thing, the chaotic variables are generated between 0 and 1 when initializing the population so that the particles are distributed uniformly in the solution space. For another thing, the chaotic sequences are generated using the Logistic mapping function in order to make chaotic search and strengthen the diversity of the population. The simulation results of several benchmark data sets of BAliBase show that the improved algorithm is effective and has good performances for the data sets with different similarity.

  4. Protein multiple sequence alignment by hybrid bio-inspired algorithms.

    PubMed

    Cutello, Vincenzo; Nicosia, Giuseppe; Pavone, Mario; Prizzi, Igor

    2011-03-01

    This article presents an immune inspired algorithm to tackle the Multiple Sequence Alignment (MSA) problem. MSA is one of the most important tasks in biological sequence analysis. Although this paper focuses on protein alignments, most of the discussion and methodology may also be applied to DNA alignments. The problem of finding the multiple alignment was investigated in the study by Bonizzoni and Vedova and Wang and Jiang, and proved to be a NP-hard (non-deterministic polynomial-time hard) problem. The presented algorithm, called Immunological Multiple Sequence Alignment Algorithm (IMSA), incorporates two new strategies to create the initial population and specific ad hoc mutation operators. It is based on the 'weighted sum of pairs' as objective function, to evaluate a given candidate alignment. IMSA was tested using both classical benchmarks of BAliBASE (versions 1.0, 2.0 and 3.0), and experimental results indicate that it is comparable with state-of-the-art multiple alignment algorithms, in terms of quality of alignments, weighted Sums-of-Pairs (SP) and Column Score (CS) values. The main novelty of IMSA is its ability to generate more than a single suboptimal alignment, for every MSA instance; this behaviour is due to the stochastic nature of the algorithm and of the populations evolved during the convergence process. This feature will help the decision maker to assess and select a biologically relevant multiple sequence alignment. Finally, the designed algorithm can be used as a local search procedure to properly explore promising alignments of the search space. PMID:21071394

  5. PSAR: measuring multiple sequence alignment reliability by probabilistic sampling

    PubMed Central

    Kim, Jaebum; Ma, Jian

    2011-01-01

    Multiple sequence alignment, which is of fundamental importance for comparative genomics, is a difficult problem and error-prone. Therefore, it is essential to measure the reliability of the alignments and incorporate it into downstream analyses. We propose a new probabilistic sampling-based alignment reliability (PSAR) score. Instead of relying on heuristic assumptions, such as the correlation between alignment quality and guide tree uncertainty in progressive alignment methods, we directly generate suboptimal alignments from an input multiple sequence alignment by a probabilistic sampling method, and compute the agreement of the input alignment with the suboptimal alignments as the alignment reliability score. We construct the suboptimal alignments by an approximate method that is based on pairwise comparisons between each single sequence and the sub-alignment of the input alignment where the chosen sequence is left out. By using simulation-based benchmarks, we find that our approach is superior to existing ones, supporting that the suboptimal alignments are highly informative source for assessing alignment reliability. We apply the PSAR method to the alignments in the UCSC Genome Browser to measure the reliability of alignments in different types of regions, such as coding exons and conserved non-coding regions, and use it to guide cross-species conservation study. PMID:21576232

  6. Improving multiple sequence alignment by using better guide trees

    PubMed Central

    2015-01-01

    Progressive sequence alignment is one of the most commonly used method for multiple sequence alignment. Roughly speaking, the method first builds a guide tree, and then aligns the sequences progressively according to the topology of the tree. It is believed that guide trees are very important to progressive alignment; a better guide tree will give an alignment with higher accuracy. Recently, we have proposed an adaptive method for constructing guide trees. This paper studies the quality of the guide trees constructed by such method. Our study showed that our adaptive method can be used to improve the accuracy of many different progressive MSA tools. In fact, we give evidences showing that the guide trees constructed by the adaptive method are among the best. PMID:25859903

  7. Quantifying the Displacement of Mismatches in Multiple Sequence Alignment Benchmarks

    PubMed Central

    Bawono, Punto; van der Velde, Arjan; Abeln, Sanne; Heringa, Jaap

    2015-01-01

    Multiple Sequence Alignment (MSA) methods are typically benchmarked on sets of reference alignments. The quality of the alignment can then be represented by the sum-of-pairs (SP) or column (CS) scores, which measure the agreement between a reference and corresponding query alignment. Both the SP and CS scores treat mismatches between a query and reference alignment as equally bad, and do not take the separation into account between two amino acids in the query alignment, that should have been matched according to the reference alignment. This is significant since the magnitude of alignment shifts is often of relevance in biological analyses, including homology modeling and MSA refinement/manual alignment editing. In this study we develop a new alignment benchmark scoring scheme, SPdist, that takes the degree of discordance of mismatches into account by measuring the sequence distance between mismatched residue pairs in the query alignment. Using this new score along with the standard SP score, we investigate the discriminatory behavior of the new score by assessing how well six different MSA methods perform with respect to BAliBASE reference alignments. The SP score and the SPdist score yield very similar outcomes when the reference and query alignments are close. However, for more divergent reference alignments the SPdist score is able to distinguish between methods that keep alignments approximately close to the reference and those exhibiting larger shifts. We observed that by using SPdist together with SP scoring we were able to better delineate the alignment quality difference between alternative MSA methods. With a case study we exemplify why it is important, from a biological perspective, to consider the separation of mismatches. The SPdist scoring scheme has been implemented in the VerAlign web server (http://www.ibi.vu.nl/programs/veralignwww/). The code for calculating SPdist score is also available upon request. PMID:25993129

  8. Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment

    PubMed Central

    Kam, Alfred; Kwak, Daniel; Leung, Clarence; Wu, Chu; Zarour, Eleyine; Sarmenta, Luis; Blanchette, Mathieu; Waldispühl, Jérôme

    2012-01-01

    Background Comparative genomics, or the study of the relationships of genome structure and function across different species, offers a powerful tool for studying evolution, annotating genomes, and understanding the causes of various genetic disorders. However, aligning multiple sequences of DNA, an essential intermediate step for most types of analyses, is a difficult computational task. In parallel, citizen science, an approach that takes advantage of the fact that the human brain is exquisitely tuned to solving specific types of problems, is becoming increasingly popular. There, instances of hard computational problems are dispatched to a crowd of non-expert human game players and solutions are sent back to a central server. Methodology/Principal Findings We introduce Phylo, a human-based computing framework applying “crowd sourcing” techniques to solve the Multiple Sequence Alignment (MSA) problem. The key idea of Phylo is to convert the MSA problem into a casual game that can be played by ordinary web users with a minimal prior knowledge of the biological context. We applied this strategy to improve the alignment of the promoters of disease-related genes from up to 44 vertebrate species. Since the launch in November 2010, we received more than 350,000 solutions submitted from more than 12,000 registered users. Our results show that solutions submitted contributed to improving the accuracy of up to 70% of the alignment blocks considered. Conclusions/Significance We demonstrate that, combined with classical algorithms, crowd computing techniques can be successfully used to help improving the accuracy of MSA. More importantly, we show that an NP-hard computational problem can be embedded in casual game that can be easily played by people without significant scientific training. This suggests that citizen science approaches can be used to exploit the billions of “human-brain peta-flops” of computation that are spent every day playing games. Phylo is

  9. Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods

    PubMed Central

    Pervez, Muhammad Tariq; Babar, Masroor Ellahi; Nadeem, Asif; Aslam, Muhammad; Awan, Ali Raza; Aslam, Naeem; Hussain, Tanveer; Naveed, Nasir; Qadri, Salman; Waheed, Usman; Shoaib, Muhammad

    2014-01-01

    A comparison of 10 most popular Multiple Sequence Alignment (MSA) tools, namely, MUSCLE, MAFFT(L-INS-i), MAFFT (FFT-NS-2), T-Coffee, ProbCons, SATe, Clustal Omega, Kalign, Multalin, and Dialign-TX is presented. We also focused on the significance of some implementations embedded in algorithm of each tool. Based on 10 simulated trees of different number of taxa generated by R, 400 known alignments and sequence files were constructed using indel-Seq-Gen. A total of 4000 test alignments were generated to study the effect of sequence length, indel size, deletion rate, and insertion rate. Results showed that alignment quality was highly dependent on the number of deletions and insertions in the sequences and that the sequence length and indel size had a weaker effect. Overall, ProbCons was consistently on the top of list of the evaluated MSA tools. SATe, being little less accurate, was 529.10% faster than ProbCons and 236.72% faster than MAFFT(L-INS-i). Among other tools, Kalign and MUSCLE achieved the highest sum of pairs. We also considered BALiBASE benchmark datasets and the results relative to BAliBASE- and indel-Seq-Gen-generated alignments were consistent in the most cases. PMID:25574120

  10. IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

    PubMed

    Pervez, Muhammad Tariq; Babar, Masroor Ellahi; Nadeem, Asif; Aslam, Naeem; Naveed, Nasir; Ahmad, Sarfraz; Muhammad, Shah; Qadri, Salman; Shahid, Muhammad; Hussain, Tanveer; Javed, Maryam

    2015-01-01

    IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix. PMID:25861209

  11. IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments

    PubMed Central

    Pervez, Muhammad Tariq; Babar, Masroor Ellahi; Nadeem, Asif; Aslam, Naeem; Naveed, Nasir; Ahmad, Sarfraz; Muhammad, Shah; Qadri, Salman; Shahid, Muhammad; Hussain, Tanveer; Javed, Maryam

    2015-01-01

    IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix. PMID:25861209

  12. Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have developed Look-Align, an interactive web-based viewer to display pre-computed multiple sequence alignments. Although initially developed to support the visualization needs of the maize diversity website Panzea (http://www.panzea.org), the viewer is a generic stand-alone tool that can be easi...

  13. Score distributions of gapped multiple sequence alignments down to the low-probability tail.

    PubMed

    Fieth, Pascal; Hartmann, Alexander K

    2016-08-01

    Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the biologically relevant high-scoring region, where the probabilities are exponentially small. For gapless local alignments of infinitely long sequences this distribution is known analytically to follow a Gumbel distribution. Distributions for gapped local alignments and global alignments of finite lengths can only be obtained numerically. To obtain result for the small-probability region, specific statistical mechanics-based rare-event algorithms can be applied. In previous studies, this was achieved for pairwise alignments. They showed that, contrary to results from previous simple sampling studies, strong deviations from the Gumbel distribution occur in case of finite sequence lengths. Here we extend the studies to multiple sequence alignments with gaps, which are much more relevant for practical applications in molecular biology. We study the distributions of scores over a large range of the support, reaching probabilities as small as 10^{-160}, for global and local (sum-of-pair scores) multiple alignments. We find that even after suitable rescaling, eliminating the sequence-length dependence, the distributions for multiple alignment differ from the pairwise alignment case. Furthermore, we also show that the previously discussed Gaussian correction to the Gumbel distribution needs to be refined, also for the case of pairwise alignments. PMID:27627266

  14. A Convex Atomic-Norm Approach to Multiple Sequence Alignment and Motif Discovery

    PubMed Central

    Yen, Ian E. H.; Lin, Xin; Zhang, Jiong; Ravikumar, Pradeep; Dhillon, Inderjit S.

    2016-01-01

    Multiple Sequence Alignment and Motif Discovery, known as NP-hard problems, are two fundamental tasks in Bioinformatics. Existing approaches to these two problems are based on either local search methods such as Expectation Maximization (EM), Gibbs Sampling or greedy heuristic methods. In this work, we develop a convex relaxation approach to both problems based on the recent concept of atomic norm and develop a new algorithm, termed Greedy Direction Method of Multiplier, for solving the convex relaxation with two convex atomic constraints. Experiments show that our convex relaxation approach produces solutions of higher quality than those standard tools widely-used in Bioinformatics community on the Multiple Sequence Alignment and Motif Discovery problems. PMID:27559428

  15. DIALIGN at GOBICS—multiple sequence alignment using various sources of external information

    PubMed Central

    Al Ait, Layal; Yamak, Zaher; Morgenstern, Burkhard

    2013-01-01

    DIALIGN is an established tool for multiple sequence alignment that is particularly useful to detect local homologies in sequences with low overall similarity. In recent years, various versions of the program have been developed, some of which are fully automated, whereas others are able to accept user-specified external information. In this article, we review some versions of the program that are available through ‘Göttingen Bioinformatics Compute Server’. In addition to previously described implementations, we present a new release of DIALIGN called ‘DIALIGN-PFAM’, which uses hits to the PFAM database for improved protein alignment. Our software is available through http://dialign.gobics.de/. PMID:23620293

  16. The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment

    PubMed Central

    Altschul, Stephen F.; Wootton, John C.; Zaslavsky, Elena; Yu, Yi-Kuo

    2010-01-01

    Most pairwise and multiple sequence alignment programs seek alignments with optimal scores. Central to defining such scores is selecting a set of substitution scores for aligned amino acids or nucleotides. For local pairwise alignment, substitution scores are implicitly of log-odds form. We now extend the log-odds formalism to multiple alignments, using Bayesian methods to construct “BILD” (“Bayesian Integral Log-odds”) substitution scores from prior distributions describing columns of related letters. This approach has been used previously only to define scores for aligning individual sequences to sequence profiles, but it has much broader applicability. We describe how to calculate BILD scores efficiently, and illustrate their uses in Gibbs sampling optimization procedures, gapped alignment, and the construction of hidden Markov model profiles. BILD scores enable automated selection of optimal motif and domain model widths, and can inform the decision of whether to include a sequence in a multiple alignment, and the selection of insertion and deletion locations. Other applications include the classification of related sequences into subfamilies, and the definition of profile-profile alignment scores. Although a fully realized multiple alignment program must rely upon more than substitution scores, many existing multiple alignment programs can be modified to employ BILD scores. We illustrate how simple BILD score based strategies can enhance the recognition of DNA binding domains, including the Api-AP2 domain in Toxoplasma gondii and Plasmodium falciparum. PMID:20657661

  17. A simple method to control over-alignment in the MAFFT multiple sequence alignment program

    PubMed Central

    Katoh, Kazutaka; Standley, Daron M.

    2016-01-01

    Motivation: We present a new feature of the MAFFT multiple alignment program for suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly sensitive in aligning conserved regions in remote homologs, but the risk of over-alignment is recently becoming greater, as low-quality or noisy sequences are increasing in protein sequence databases, due, for example, to sequencing errors and difficulty in gene prediction. Results: The proposed method utilizes a variable scoring matrix for different pairs of sequences (or groups) in a single multiple sequence alignment, based on the global similarity of each pair. This method significantly increases the correctly gapped sites in real examples and in simulations under various conditions. Regarding sensitivity, the effect of the proposed method is slightly negative in real protein-based benchmarks, and mostly neutral in simulation-based benchmarks. This approach is based on natural biological reasoning and should be compatible with many methods based on dynamic programming for multiple sequence alignment. Availability and implementation: The new feature is available in MAFFT versions 7.263 and higher. http://mafft.cbrc.jp/alignment/software/ Contact: katoh@ifrec.osaka-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153688

  18. An enhanced algorithm for multiple sequence alignment of protein sequences using genetic algorithm

    PubMed Central

    Kumar, Manish

    2015-01-01

    One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this paper, an alignment method using genetic algorithm for multiple sequence alignment has been proposed. Two different genetic operators mainly crossover and mutation were defined and implemented with the proposed method in order to know the population evolution and quality of the sequence aligned. The proposed method is assessed with protein benchmark dataset, e.g., BALIBASE, by comparing the obtained results to those obtained with other alignment algorithms, e.g., SAGA, RBT-GA, PRRP, HMMT, SB-PIMA, CLUSTALX, CLUSTAL W, DIALIGN and PILEUP8 etc. Experiments on a wide range of data have shown that the proposed algorithm is much better (it terms of score) than previously proposed algorithms in its ability to achieve high alignment quality. PMID:27065770

  19. An enhanced algorithm for multiple sequence alignment of protein sequences using genetic algorithm.

    PubMed

    Kumar, Manish

    2015-01-01

    One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this paper, an alignment method using genetic algorithm for multiple sequence alignment has been proposed. Two different genetic operators mainly crossover and mutation were defined and implemented with the proposed method in order to know the population evolution and quality of the sequence aligned. The proposed method is assessed with protein benchmark dataset, e.g., BALIBASE, by comparing the obtained results to those obtained with other alignment algorithms, e.g., SAGA, RBT-GA, PRRP, HMMT, SB-PIMA, CLUSTALX, CLUSTAL W, DIALIGN and PILEUP8 etc. Experiments on a wide range of data have shown that the proposed algorithm is much better (it terms of score) than previously proposed algorithms in its ability to achieve high alignment quality. PMID:27065770

  20. TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction

    PubMed Central

    Chang, Jia-Ming; Di Tommaso, Paolo; Lefort, Vincent; Gascuel, Olivier; Notredame, Cedric

    2015-01-01

    This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. The evaluation can be used to identify the aligned positions most likely to contain structurally analogous residues and also most likely to support an accurate phylogenetic reconstruction. The TCS scoring scheme has been shown to be accurate predictor of structural alignment correctness among commonly used methods. It has also been shown to outperform common filtering schemes like Gblocks or trimAl when doing MSA post-processing prior to phylogenetic tree reconstruction. The web server is available from http://tcoffee.crg.cat/tcs. PMID:25855806

  1. MSA-PAD: DNA multiple sequence alignment framework based on PFAM accessed domain information.

    PubMed

    Balech, Bachir; Vicario, Saverio; Donvito, Giacinto; Monaco, Alfonso; Notarangelo, Pasquale; Pesole, Graziano

    2015-08-01

    Here we present the MSA-PAD application, a DNA multiple sequence alignment framework that uses PFAM protein domain information to align DNA sequences encoding either single or multiple protein domains. MSA-PAD has two alignment options: gene and genome mode. PMID:25819080

  2. A tabu search algorithm for post-processing multiple sequence alignment.

    PubMed

    Riaz, Tariq; Yi, Wang; Li, Kuo-Bin

    2005-02-01

    Tabu search is a meta-heuristic approach that is proven to be useful in solving combinatorial optimization problems. We implement the adaptive memory features of tabu search to refine a multiple sequence alignment. Adaptive memory helps the search process to avoid local optima and explores the solution space economically and effectively without getting trapped into cycles. The algorithm is further enhanced by introducing extended tabu search features such as intensification and diversification. The neighborhoods of a solution are generated stochastically and a consistency-based objective function is employed to measure its quality. The algorithm is tested with the datasets from BAliBASE benchmarking database. We have observed through experiments that tabu search is able to improve the quality of multiple alignments generated by other software such as ClustalW and T-Coffee. The source code of our algorithm is available at http://www.bii.a-star.edu.sg/~tariq/tabu/. PMID:15751117

  3. A novel approach to multiple sequence alignment using hadoop data grids.

    PubMed

    Sudha Sadasivam, G; Baktavatchalam, G

    2010-01-01

    Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we propose a time efficient approach to sequence alignment that also produces quality alignment. The dynamic nature of the algorithm coupled with data and computational parallelism of hadoop data grids improves the accuracy and speed of sequence alignment. The principle of block splitting in hadoop coupled with its scalability facilitates alignment of very large sequences. PMID:21224205

  4. Upcoming challenges for multiple sequence alignment methods in the high-throughput era

    PubMed Central

    Kemena, Carsten; Notredame, Cedric

    2009-01-01

    This review focuses on recent trends in multiple sequence alignment tools. It describes the latest algorithmic improvements including the extension of consistency-based methods to the problem of template-based multiple sequence alignments. Some results are presented suggesting that template-based methods are significantly more accurate than simpler alternative methods. The validation of existing methods is also discussed at length with the detailed description of recent results and some suggestions for future validation strategies. The last part of the review addresses future challenges for multiple sequence alignment methods in the genomic era, most notably the need to cope with very large sequences, the need to integrate large amounts of experimental data, the need to accurately align non-coding and non-transcribed sequences and finally, the need to integrate many alternative methods and approaches. Contact: cedric.notredame@crg.es PMID:19648142

  5. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

    PubMed Central

    Sievers, Fabian; Wilm, Andreas; Dineen, David; Gibson, Toby J; Karplus, Kevin; Li, Weizhong; Lopez, Rodrigo; McWilliam, Hamish; Remmert, Michael; Söding, Johannes; Thompson, Julie D; Higgins, Desmond G

    2011-01-01

    Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam. PMID:21988835

  6. Multiple sequence alignment: a major challenge to large-scale phylogenetics

    PubMed Central

    Liu, Kevin; Linder, C. Randal; Warnow, Tandy

    2011-01-01

    Over the last decade, dramatic advances have been made in developing methods for large-scale phylogeny estimation, so that it is now feasible for investigators with moderate computational resources to obtain reasonable solutions to maximum likelihood and maximum parsimony, even for datasets with a few thousand sequences. There has also been progress on developing methods for multiple sequence alignment, so that greater alignment accuracy (and subsequent improvement in phylogenetic accuracy) is now possible through automated methods. However, these methods have not been tested under conditions that reflect properties of datasets confronted by large-scale phylogenetic estimation projects. In this paper we report on a study that compares several alignment methods on a benchmark collection of nucleotide sequence datasets of up to 78,132 sequences. We show that as the number of sequences increases, the number of alignment methods that can analyze the datasets decreases. Furthermore, the most accurate alignment methods are unable to analyze the very largest datasets we studied, so that only moderately accurate alignment methods can be used on the largest datasets. As a result, alignments computed for large datasets have relatively large error rates, and maximum likelihood phylogenies computed on these alignments also have high error rates. Therefore, the estimation of highly accurate multiple sequence alignments is a major challenge for Tree of Life projects, and more generally for large-scale systematics studies. PMID:21113338

  7. Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

    PubMed Central

    Tan, Ge; Muffato, Matthieu; Ledergerber, Christian; Herrero, Javier; Goldman, Nick; Gil, Manuel; Dessimoz, Christophe

    2015-01-01

    Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts of the alignment. In recent years several automated filtering approaches have been proposed, but despite their popularity, a systematic and comprehensive comparison of different alignment filtering methods on real data has been lacking. Here, we extend and apply recently introduced phylogenetic tests of alignment accuracy on a large number of gene families and contrast the performance of unfiltered versus filtered alignments in the context of single-gene phylogeny reconstruction. Based on multiple genome-wide empirical and simulated data sets, we show that the trees obtained from filtered MSAs are on average worse than those obtained from unfiltered MSAs. Furthermore, alignment filtering often leads to an increase in the proportion of well-supported branches that are actually wrong. We confirm that our findings hold for a wide range of parameters and methods. Although our results suggest that light filtering (up to 20% of alignment positions) has little impact on tree accuracy and may save some computation time, contrary to widespread practice, we do not generally recommend the use of current alignment filtering methods for phylogenetic inference. By providing a way to rigorously and systematically measure the impact of filtering on alignments, the methodology set forth here will guide the development of better filtering algorithms. PMID:26031838

  8. Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.

    PubMed

    Tan, Ge; Muffato, Matthieu; Ledergerber, Christian; Herrero, Javier; Goldman, Nick; Gil, Manuel; Dessimoz, Christophe

    2015-09-01

    Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts of the alignment. In recent years several automated filtering approaches have been proposed, but despite their popularity, a systematic and comprehensive comparison of different alignment filtering methods on real data has been lacking. Here, we extend and apply recently introduced phylogenetic tests of alignment accuracy on a large number of gene families and contrast the performance of unfiltered versus filtered alignments in the context of single-gene phylogeny reconstruction. Based on multiple genome-wide empirical and simulated data sets, we show that the trees obtained from filtered MSAs are on average worse than those obtained from unfiltered MSAs. Furthermore, alignment filtering often leads to an increase in the proportion of well-supported branches that are actually wrong. We confirm that our findings hold for a wide range of parameters and methods. Although our results suggest that light filtering (up to 20% of alignment positions) has little impact on tree accuracy and may save some computation time, contrary to widespread practice, we do not generally recommend the use of current alignment filtering methods for phylogenetic inference. By providing a way to rigorously and systematically measure the impact of filtering on alignments, the methodology set forth here will guide the development of better filtering algorithms. PMID:26031838

  9. Multiple sequence alignment algorithm based on a dispersion graph and ant colony algorithm.

    PubMed

    Chen, Weiyang; Liao, Bo; Zhu, Wen; Xiang, Xuyu

    2009-10-01

    In this article, we describe a representation for the processes of multiple sequences alignment (MSA) and used it to solve the problem of MSA. By this representation, we took every possible aligning result into account by defining the representation of gap insertion, the value of heuristic information in every optional path and scoring rule. On the basis of the proposed multidimensional graph, we used the ant colony algorithm to find the better path that denotes a better aligning result. In our article, we proposed the instance of three-dimensional graph and four-dimensional graph and advanced a special ichnographic representation to analyze MSA. It is yet only an experimental software, and we gave an example for finding the best aligning result by three-dimensional graph and ant colony algorithm. Experimental results show that our method can improve the solution quality on MSA benchmarks. PMID:19130503

  10. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

    PubMed

    Cannone, Jamie J; Sweeney, Blake A; Petrov, Anton I; Gutell, Robin R; Zirbel, Craig L; Leontis, Neocles

    2015-07-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

  11. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server

    PubMed Central

    Cannone, Jamie J.; Sweeney, Blake A.; Petrov, Anton I.; Gutell, Robin R.; Zirbel, Craig L.; Leontis, Neocles

    2015-01-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

  12. Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment.

    PubMed

    Kwak, Daniel; Kam, Alfred; Becerra, David; Zhou, Qikuan; Hops, Adam; Zarour, Eleyine; Kam, Arthur; Sarmenta, Luis; Blanchette, Mathieu; Waldispühl, Jérôme

    2013-01-01

    Citizen science games such as Galaxy Zoo, Foldit, and Phylo aim to harness the intelligence and processing power generated by crowds of online gamers to solve scientific problems. However, the selection of the data to be analyzed through these games is under the exclusive control of the game designers, and so are the results produced by gamers. Here, we introduce Open-Phylo, a freely accessible crowd-computing platform that enables any scientist to enter our system and use crowds of gamers to assist computer programs in solving one of the most fundamental problems in genomics: the multiple sequence alignment problem. PMID:24148814

  13. Large-Scale Multiple Sequence Alignment and Tree Estimation Using SATé

    PubMed Central

    Liu, Kevin; Warnow, Tandy

    2016-01-01

    SATé is a method for estimating multiple sequence alignments and trees that has been shown to produce highly accurate results for datasets with large numbers of sequences. Running SATé using its default settings is very simple, but improved accuracy can be obtained by modifying its algorithmic parameters. We provide a detailed introduction to the algorithmic approach used by SATé, and instructions for running a SATé analysis using the GUI under default settings. We also provide a discussion of how to modify these settings to obtain improved results, and how to use SATé in a phylogenetic analysis pipeline. PMID:24170406

  14. KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins

    PubMed Central

    Lange, Joanna; Wyrwicz, Lucjan S.; Vriend, Gert

    2016-01-01

    Summary: Intrinsically disordered proteins (IDPs) lack tertiary structure and thus differ from globular proteins in terms of their sequence–structure–function relations. IDPs have lower sequence conservation, different types of active sites and a different distribution of functionally important regions, which altogether make their multiple sequence alignment (MSA) difficult. The KMAD MSA software has been written specifically for the alignment and annotation of IDPs. It augments the substitution matrix with knowledge about post-translational modifications, functional domains and short linear motifs. Results: MSAs produced with KMAD describe well-conserved features among IDPs, tend to agree well with biological intuition, and are a good basis for designing new experiments to shed light on this large, understudied class of proteins. Availability and implementation: KMAD web server is accessible at http://www.cmbi.ru.nl/kmad/. A standalone version is freely available. Contact: vriend@cmbi.ru.nl PMID:26568635

  15. Multiple sequence alignment based on combining genetic algorithm with chaotic sequences.

    PubMed

    Gao, C; Wang, B; Zhou, C J; Zhang, Q

    2016-01-01

    In bioinformatics, sequence alignment is one of the most common problems. Multiple sequence alignment is an NP (nondeterministic polynomial time) problem, which requires further study and exploration. The chaos optimization algorithm is a type of chaos theory, and a procedure for combining the genetic algorithm (GA), which uses ergodicity, and inherent randomness of chaotic iteration. It is an efficient method to solve the basic premature phenomenon of the GA. Applying the Logistic map to the GA and using chaotic sequences to carry out the chaotic perturbation can improve the convergence of the basic GA. In addition, the random tournament selection and optimal preservation strategy are used in the GA. Experimental evidence indicates good results for this process. PMID:27420977

  16. SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

    PubMed Central

    Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver

    2012-01-01

    Motivation: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. Results: In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Availability: Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license. Contact: epruesse@mpi-bremen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22556368

  17. A parallel approach of COFFEE objective function to multiple sequence alignment

    NASA Astrophysics Data System (ADS)

    Zafalon, G. F. D.; Visotaky, J. M. V.; Amorim, A. R.; Valêncio, C. R.; Neves, L. A.; de Souza, R. C. G.; Machado, J. M.

    2015-09-01

    The computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.

  18. Determining Word Sequence Variation Patterns in Clinical Documents using Multiple Sequence Alignment

    PubMed Central

    Meng, Frank; Morioka, Craig A.; El-Saden, Suzie

    2011-01-01

    Sentences and phrases that represent a certain meaning often exhibit patterns of variation where they differ from a basic structural form by one or two words. We present an algorithm that utilizes multiple sequence alignments (MSAs) to generate a representation of groups of phrases that possess the same semantic meaning but also share in common the same basic word sequence structure. The MSA enables the determination not only of the words that compose the basic word sequence, but also of the locations within the structure that exhibit variation. The algorithm can be utilized to generate patterns of text sequences that can be used as the basis for a pattern-based classifier, as a starting point to bootstrap the pattern building process for a regular expression-based classifiers, or serve to reveal the variation characteristics of sentences and phrases within a particular domain. PMID:22195152

  19. Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)

    PubMed Central

    Martin, Andrew C. R.

    2014-01-01

    The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and ’dotifying’ repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/. PMID:25653836

  20. Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

    PubMed

    Martin, Andrew C R

    2014-01-01

    The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/. PMID:25653836

  1. ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments

    PubMed Central

    Schwarz, Roland F.; Tamuri, Asif U.; Kultys, Marek; King, James; Godwin, James; Florescu, Ana M.; Schultz, Jörg; Goldman, Nick

    2016-01-01

    Sequence Logos and its variants are the most commonly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs. They provide consensus-based summaries of the sequences in the alignment. Consequently, individual sequences cannot be identified in the visualization and covariant sites are not easily discernible. We recently proposed Sequence Bundles, a motif visualization technique that maintains a one-to-one relationship between sequences and their graphical representation and visualizes covariant sites. We here present Alvis, an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the power of the visualization method with an interactive toolkit allowing detection of covariant sites, annotation of trees with synapomorphies and homoplasies, and motif detection. It also offers numerical analysis functionality, such as dimension reduction and classification. Alvis is user-friendly, highly customizable and can export results in publication-quality figures. It is available as a full-featured standalone version (http://www.bitbucket.org/rfs/alvis) and its Sequence Bundles visualization module is further available as a web application (http://science-practice.com/projects/sequence-bundles). PMID:26819408

  2. ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.

    PubMed

    Schwarz, Roland F; Tamuri, Asif U; Kultys, Marek; King, James; Godwin, James; Florescu, Ana M; Schultz, Jörg; Goldman, Nick

    2016-05-01

    Sequence Logos and its variants are the most commonly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs. They provide consensus-based summaries of the sequences in the alignment. Consequently, individual sequences cannot be identified in the visualization and covariant sites are not easily discernible. We recently proposed Sequence Bundles, a motif visualization technique that maintains a one-to-one relationship between sequences and their graphical representation and visualizes covariant sites. We here present Alvis, an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the power of the visualization method with an interactive toolkit allowing detection of covariant sites, annotation of trees with synapomorphies and homoplasies, and motif detection. It also offers numerical analysis functionality, such as dimension reduction and classification. Alvis is user-friendly, highly customizable and can export results in publication-quality figures. It is available as a full-featured standalone version (http://www.bitbucket.org/rfs/alvis) and its Sequence Bundles visualization module is further available as a web application (http://science-practice.com/projects/sequence-bundles). PMID:26819408

  3. Evidence of Statistical Inconsistency of Phylogenetic Methods in the Presence of Multiple Sequence Alignment Uncertainty

    PubMed Central

    Md Mukarram Hossain, A.S.; Blackburne, Benjamin P.; Shah, Abhijeet; Whelan, Simon

    2015-01-01

    Evolutionary studies usually use a two-step process to investigate sequence data. Step one estimates a multiple sequence alignment (MSA) and step two applies phylogenetic methods to ask evolutionary questions of that MSA. Modern phylogenetic methods infer evolutionary parameters using maximum likelihood or Bayesian inference, mediated by a probabilistic substitution model that describes sequence change over a tree. The statistical properties of these methods mean that more data directly translates to an increased confidence in downstream results, providing the substitution model is adequate and the MSA is correct. Many studies have investigated the robustness of phylogenetic methods in the presence of substitution model misspecification, but few have examined the statistical properties of those methods when the MSA is unknown. This simulation study examines the statistical properties of the complete two-step process when inferring sequence divergence and the phylogenetic tree topology. Both nucleotide and amino acid analyses are negatively affected by the alignment step, both through inaccurate guide tree estimates and through overfitting to that guide tree. For many alignment tools these effects become more pronounced when additional sequences are added to the analysis. Nucleotide sequences are particularly susceptible, with MSA errors leading to statistical support for long-branch attraction artifacts, which are usually associated with gross substitution model misspecification. Amino acid MSAs are more robust, but do tend to arbitrarily resolve multifurcations in favor of the guide tree. No inference strategies produce consistently accurate estimates of divergence between sequences, although amino acid MSAs are again more accurate than their nucleotide counterparts. We conclude with some practical suggestions about how to limit the effect of MSA uncertainty on evolutionary inference. PMID:26139831

  4. RBT-GA: a novel metaheuristic for solving the multiple sequence alignment problem

    PubMed Central

    Taheri, Javid; Zomaya, Albert Y

    2009-01-01

    Background Multiple Sequence Alignment (MSA) has always been an active area of research in Bioinformatics. MSA is mainly focused on discovering biologically meaningful relationships among different sequences or proteins in order to investigate the underlying main characteristics/functions. This information is also used to generate phylogenetic trees. Results This paper presents a novel approach, namely RBT-GA, to solve the MSA problem using a hybrid solution methodology combining the Rubber Band Technique (RBT) and the Genetic Algorithm (GA) metaheuristic. RBT is inspired by the behavior of an elastic Rubber Band (RB) on a plate with several poles, which is analogues to locations in the input sequences that could potentially be biologically related. A GA attempts to mimic the evolutionary processes of life in order to locate optimal solutions in an often very complex landscape. RBT-GA is a population based optimization algorithm designed to find the optimal alignment for a set of input protein sequences. In this novel technique, each alignment answer is modeled as a chromosome consisting of several poles in the RBT framework. These poles resemble locations in the input sequences that are most likely to be correlated and/or biologically related. A GA-based optimization process improves these chromosomes gradually yielding a set of mostly optimal answers for the MSA problem. Conclusion RBT-GA is tested with one of the well-known benchmarks suites (BALiBASE 2.0) in this area. The obtained results show that the superiority of the proposed technique even in the case of formidable sequences. PMID:19594869

  5. Multidimensional mutual information methods for the analysis of covariation in multiple sequence alignments

    PubMed Central

    2014-01-01

    Background Several methods are available for the detection of covarying positions from a multiple sequence alignment (MSA). If the MSA contains a large number of sequences, information about the proximities between residues derived from covariation maps can be sufficient to predict a protein fold. However, in many cases the structure is already known, and information on the covarying positions can be valuable to understand the protein mechanism and dynamic properties. Results In this study we have sought to determine whether a multivariate (multidimensional) extension of traditional mutual information (MI) can be an additional tool to study covariation. The performance of two multidimensional MI (mdMI) methods, designed to remove the effect of ternary/quaternary interdependencies, was tested with a set of 9 MSAs each containing <400 sequences, and was shown to be comparable to that of the newest methods based on maximum entropy/pseudolikelyhood statistical models of protein sequences. However, while all the methods tested detected a similar number of covarying pairs among the residues separated by < 8 Å in the reference X-ray structures, there was on average less than 65% overlap between the top scoring pairs detected by methods that are based on different principles. Conclusions Given the large variety of structure and evolutionary history of different proteins it is possible that a single best method to detect covariation in all proteins does not exist, and that for each protein family the best information can be derived by merging/comparing results obtained with different methods. This approach may be particularly valuable in those cases in which the size of the MSA is small or the quality of the alignment is low, leading to significant differences in the pairs detected by different methods. PMID:24886131

  6. CUDA ClustalW: An efficient parallel algorithm for progressive multiple sequence alignment on Multi-GPUs.

    PubMed

    Hung, Che-Lun; Lin, Yu-Shiang; Lin, Chun-Yuan; Chung, Yeh-Ching; Chung, Yi-Fang

    2015-10-01

    For biological applications, sequence alignment is an important strategy to analyze DNA and protein sequences. Multiple sequence alignment is an essential methodology to study biological data, such as homology modeling, phylogenetic reconstruction and etc. However, multiple sequence alignment is a NP-hard problem. In the past decades, progressive approach has been proposed to successfully align multiple sequences by adopting iterative pairwise alignments. Due to rapid growth of the next generation sequencing technologies, a large number of sequences can be produced in a short period of time. When the problem instance is large, progressive alignment will be time consuming. Parallel computing is a suitable solution for such applications, and GPU is one of the important architectures for contemporary parallel computing researches. Therefore, we proposed a GPU version of ClustalW v2.0.11, called CUDA ClustalW v1.0, in this work. From the experiment results, it can be seen that the CUDA ClustalW v1.0 can achieve more than 33× speedups for overall execution time by comparing to ClustalW v2.0.11. PMID:26052076

  7. Two Simple and Efficient Algorithms to Compute the SP-Score Objective Function of a Multiple Sequence Alignment

    PubMed Central

    Ranwez, Vincent

    2016-01-01

    Background Multiple sequence alignment (MSA) is a crucial step in many molecular analyses and many MSA tools have been developed. Most of them use a greedy approach to construct a first alignment that is then refined by optimizing the sum of pair score (SP-score). The SP-score estimation is thus a bottleneck for most MSA tools since it is repeatedly required and is time consuming. Results Given an alignment of n sequences and L sites, I introduce here optimized solutions reaching O(nL) time complexity for affine gap cost, instead of O(n2L), which are easy to implement. PMID:27505054

  8. New Challenges of the Computation of Multiple Sequence Alignments in the High-Throughput Era (2010 JGI/ANL HPC Workshop)

    SciTech Connect

    Notredame, Cedric

    2010-01-26

    Cedric Notredame from the Centre for Genomic Regulation gives a presentation on "New Challenges of the Computation of Multiple Sequence Alignments in the High-Throughput Era" at the JGI/Argonne HPC Workshop on January 26, 2010.

  9. New Challenges of the Computation of Multiple Sequence Alignments in the High-Throughput Era (2010 JGI/ANL HPC Workshop)

    ScienceCinema

    Notredame, Cedric [Centre for Genomic Regulation

    2011-06-08

    Cedric Notredame from the Centre for Genomic Regulation gives a presentation on "New Challenges of the Computation of Multiple Sequence Alignments in the High-Throughput Era" at the JGI/Argonne HPC Workshop on January 26, 2010.

  10. Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search

    NASA Technical Reports Server (NTRS)

    Wheeler, Ward C.

    2003-01-01

    A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

  11. Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search.

    PubMed

    Wheeler, Ward C

    2003-06-01

    A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. PMID:12901383

  12. Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.

    PubMed

    Washietl, Stefan; Bernhart, Stephan H; Kellis, Manolis

    2014-01-01

    Many biologically important RNA structures are conserved in evolution leading to characteristic mutational patterns. RNAalifold is a widely used program to predict consensus secondary structures in multiple alignments by combining evolutionary information with traditional energy-based RNA folding algorithms. Here we describe the theory and applications of the RNAalifold algorithm. Consensus secondary structure prediction not only leads to significantly more accurate structure models, but it also allows to study structural conservation of functional RNAs. PMID:24639158

  13. PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL

    PubMed Central

    2012-01-01

    Background In recent years, an exponential growing number of tools for protein sequence analysis, editing and modeling tasks have been put at the disposal of the scientific community. Despite the vast majority of these tools have been released as open source software, their deep learning curves often discourages even the most experienced users. Results A simple and intuitive interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., [PSI-]BLAST, ClustalW, MUSCLE, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks. Sequence similarity searches, multiple sequence and structural alignments generation and editing, and even the possibility to merge sequence and structure alignments have been implemented in PyMod, with the aim of creating a simple, yet powerful tool for sequence and structure analysis and building of homology models. Conclusions PyMod represents a new tool for the analysis and the manipulation of protein sequences and structures. The ease of use, integration with many sequence retrieving and alignment tools and PyMOL, one of the most used molecular visualization system, are the key features of this tool. Source code, installation instructions, video tutorials and a user's guide are freely available at the URL http://schubert.bio.uniroma1.it/pymod/index.html PMID:22536966

  14. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

    PubMed

    Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

    2016-07-01

    The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. PMID:27106060

  15. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

    PubMed Central

    Di Tommaso, Paolo; Moretti, Sebastien; Xenarios, Ioannis; Orobitg, Miquel; Montanyola, Alberto; Chang, Jia-Ming; Taly, Jean-François; Notredame, Cedric

    2011-01-01

    This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat. PMID:21558174

  16. Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis

    PubMed Central

    Aniba, Mohamed Radhouene; Siguenza, Sophie; Friedrich, Anne; Plewniak, Frédéric; Poch, Olivier; Marchler-Bauer, Aron

    2009-01-01

    The traditional approach to bioinformatics analyses relies on independent task-specific services and applications, using different input and output formats, often idiosyncratic, and frequently not designed to inter-operate. In general, such analyses were performed by experts who manually verified the results obtained at each step in the process. Today, the amount of bioinformatics information continuously being produced means that handling the various applications used to study this information presents a major data management and analysis challenge to researchers. It is now impossible to manually analyse all this information and new approaches are needed that are capable of processing the large-scale heterogeneous data in order to extract the pertinent information. We review the recent use of integrated expert systems aimed at providing more efficient knowledge extraction for bioinformatics research. A general methodology for building knowledge-based expert systems is described, focusing on the unstructured information management architecture, UIMA, which provides facilities for both data and process management. A case study involving a multiple alignment expert system prototype called AlexSys is also presented. PMID:18971242

  17. Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments.

    PubMed

    Ortiz, A R; Kolinski, A; Skolnick, J

    1998-02-15

    Using a recently developed protein folding algorithm, a prediction of the tertiary structure of the KIX domain of the CREB binding protein is described. The method incorporates predicted secondary and tertiary restraints derived from multiple sequence alignments in a reduced protein model whose conformational space is explored by Monte Carlo dynamics. Secondary structure restraints are provided by the PHD secondary structure prediction algorithm that was modified for the presence of predicted U-turns, i.e., regions where the chain reverses global direction. Tertiary restraints are obtained via a two-step process: First, seed side-chain contacts are identified from a correlated mutation analysis, and then, a threading-based algorithm expands the number of these seed contacts. Blind predictions indicate that the KIX domain is a putative three-helix bundle, although the chirality of the bundle could not be uniquely determined. The expected root-mean-square deviation for the correct chirality of the KIX domain is between 5.0 and 6.2 A. This is to be compared with the estimate of 12.9 A that would be expected by a random prediction, using the model of F. Cohen and M. Sternberg (J. Mol. Biol. 138:321-333, 1980). PMID:9517544

  18. MC64-ClustalWP2: a highly-parallel hybrid strategy to align multiple sequences in many-core architectures.

    PubMed

    Díaz, David; Esteban, Francisco J; Hernández, Pilar; Caballero, Juan Antonio; Guevara, Antonio; Dorado, Gabriel; Gálvez, Sergio

    2014-01-01

    We have developed the MC64-ClustalWP2 as a new implementation of the Clustal W algorithm, integrating a novel parallelization strategy and significantly increasing the performance when aligning long sequences in architectures with many cores. It must be stressed that in such a process, the detailed analysis of both the software and hardware features and peculiarities is of paramount importance to reveal key points to exploit and optimize the full potential of parallelism in many-core CPU systems. The new parallelization approach has focused into the most time-consuming stages of this algorithm. In particular, the so-called progressive alignment has drastically improved the performance, due to a fine-grained approach where the forward and backward loops were unrolled and parallelized. Another key approach has been the implementation of the new algorithm in a hybrid-computing system, integrating both an Intel Xeon multi-core CPU and a Tilera Tile64 many-core card. A comparison with other Clustal W implementations reveals the high-performance of the new algorithm and strategy in many-core CPU architectures, in a scenario where the sequences to align are relatively long (more than 10 kb) and, hence, a many-core GPU hardware cannot be used. Thus, the MC64-ClustalWP2 runs multiple alignments more than 18x than the original Clustal W algorithm, and more than 7x than the best x86 parallel implementation to date, being publicly available through a web service. Besides, these developments have been deployed in cost-effective personal computers and should be useful for life-science researchers, including the identification of identities and differences for mutation/polymorphism analyses, biodiversity and evolutionary studies and for the development of molecular markers for paternity testing, germplasm management and protection, to assist breeding, illegal traffic control, fraud prevention and for the protection of the intellectual property (identification

  19. MC64-ClustalWP2: A Highly-Parallel Hybrid Strategy to Align Multiple Sequences in Many-Core Architectures

    PubMed Central

    Díaz, David; Esteban, Francisco J.; Hernández, Pilar; Caballero, Juan Antonio; Guevara, Antonio

    2014-01-01

    We have developed the MC64-ClustalWP2 as a new implementation of the Clustal W algorithm, integrating a novel parallelization strategy and significantly increasing the performance when aligning long sequences in architectures with many cores. It must be stressed that in such a process, the detailed analysis of both the software and hardware features and peculiarities is of paramount importance to reveal key points to exploit and optimize the full potential of parallelism in many-core CPU systems. The new parallelization approach has focused into the most time-consuming stages of this algorithm. In particular, the so-called progressive alignment has drastically improved the performance, due to a fine-grained approach where the forward and backward loops were unrolled and parallelized. Another key approach has been the implementation of the new algorithm in a hybrid-computing system, integrating both an Intel Xeon multi-core CPU and a Tilera Tile64 many-core card. A comparison with other Clustal W implementations reveals the high-performance of the new algorithm and strategy in many-core CPU architectures, in a scenario where the sequences to align are relatively long (more than 10 kb) and, hence, a many-core GPU hardware cannot be used. Thus, the MC64-ClustalWP2 runs multiple alignments more than 18x than the original Clustal W algorithm, and more than 7x than the best x86 parallel implementation to date, being publicly available through a web service. Besides, these developments have been deployed in cost-effective personal computers and should be useful for life-science researchers, including the identification of identities and differences for mutation/polymorphism analyses, biodiversity and evolutionary studies and for the development of molecular markers for paternity testing, germplasm management and protection, to assist breeding, illegal traffic control, fraud prevention and for the protection of the intellectual property (identification

  20. Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors.

    PubMed

    Oliani, L C; Lidani, K C F; Gabriel, J E

    2015-01-01

    MyoD and MyoG are transcription factors that have essential roles in myogenic lineage determination and muscle differentiation. The purpose of this study was to compare multiple amino acid sequences of myogenic regulatory proteins to infer evolutionary relationships among chordates. Protein sequences from Mus musculus (P10085 and P12979), human Homo sapiens (P15172 and P15173), bovine Bos taurus (Q7YS82 and Q7YS81), wild pig Sus scrofa (P49811 and P49812), quail Coturnix coturnix (P21572 and P34060), chicken Gallus gallus (P16075 and P17920), rat Rattus norvegicus (Q02346 and P20428), domestic water buffalo Bubalus bubalis (D2SP11 and A7L034), and sheep Ovis aries (Q90477 and D3YKV7) were searched from a non-redundant protein sequence database UniProtKB/Swiss-Prot, and subsequently analyzed using the Mega6.0 software. MyoD evolutionary analyses revealed the presence of three main clusters with all mammals branched in one cluster, members of the order Rodentia (mouse and rat) in a second branch linked to the first, and birds of the order Galliformes (chicken and quail) remaining isolated in a third. MyoG evolutionary analyses aligned sequences in two main clusters, all mammalian specimens grouped in different sub-branches, and birds clustered in a second branch. These analyses suggest that the evolution of MyoD and MyoG was driven by different pathways. PMID:26505406

  1. Analyses of the radiation of birnaviruses from diverse host phyla and of their evolutionary affinities with other double-stranded RNA and positive strand RNA viruses using robust structure-based multiple sequence alignments and advanced phylogenetic methods

    PubMed Central

    2013-01-01

    Background Birnaviruses form a distinct family of double-stranded RNA viruses infecting animals as different as vertebrates, mollusks, insects and rotifers. With such a wide host range, they constitute a good model for studying the adaptation to the host. Additionally, several lines of evidence link birnaviruses to positive strand RNA viruses and suggest that phylogenetic analyses may provide clues about transition. Results We characterized the genome of a birnavirus from the rotifer Branchionus plicalitis. We used X-ray structures of RNA-dependent RNA polymerases and capsid proteins to obtain multiple structure alignments that allowed us to obtain reliable multiple sequence alignments and we employed “advanced” phylogenetic methods to study the evolutionary relationships between some positive strand and double-stranded RNA viruses. We showed that the rotifer birnavirus genome exhibited an organization remarkably similar to other birnaviruses. As this host was phylogenetically very distant from the other known species targeted by birnaviruses, we revisited the evolutionary pathways within the Birnaviridae family using phylogenetic reconstruction methods. We also applied a number of phylogenetic approaches based on structurally conserved domains/regions of the capsid and RNA-dependent RNA polymerase proteins to study the evolutionary relationships between birnaviruses, other double-stranded RNA viruses and positive strand RNA viruses. Conclusions We show that there is a good correlation between the phylogeny of the birnaviruses and that of their hosts at the phylum level using the RNA-dependent RNA polymerase (genomic segment B) on the one hand and a concatenation of the capsid protein, protease and ribonucleoprotein (genomic segment A) on the other hand. This correlation tends to vanish within phyla. The use of advanced phylogenetic methods and robust structure-based multiple sequence alignments allowed us to obtain a more accurate picture (in terms of

  2. Dimensionality reduction via locally reconstructive patch alignment

    NASA Astrophysics Data System (ADS)

    Chen, Yi; Yin, Jun; Zhu, Jie; Jin, Zhong

    2012-07-01

    Based on the local patch concept, we proposed locally reconstructive patch alignment (LRPA) for dimensionality reduction. For each patch, LRPA aims to find the low-dimensional subspace in which the reconstruction error of the within-class nearest neighbors is minimized and the reconstruction error of the between-class nearest neighbors is maximized. LRPA preserves the local structure hidden in the high-dimensional space. More importantly, LRPA has natural connections with linear regression classification (LRC). While LRC uses reconstruction errors as the classification rule, a sample can be classified correctly when the within-class reconstruction error is minimal. The goal of LRPA makes it cooperate well with LRC. The experimental results on the extended Yale B (YALE-B), AR, PolyU finger knuckle print, and the palm print databases demonstrate LRPA plus LRC is an effective and robust pattern-recognition system.

  3. H2rs: Deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments

    PubMed Central

    2014-01-01

    for residue pairs by means of the von Neumann entropy and a p-value improved the success rate in identifying important residue positions. The integration of proven statistical concepts and normalization allows for an easier comparison of results obtained with different proteins. Comparing the outcome of the local method H2rs and of the global method PSICOV indicates that such methods supplement each other and have different scopes of application. PMID:24766829

  4. Local Structural Alignment of RNA with Affine Gap Model

    NASA Astrophysics Data System (ADS)

    Wong, Thomas K. F.; Cheung, Brenda W. Y.; Lam, T. W.; Yiu, S. M.

    Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps. In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem. Based on a preliminary experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.

  5. R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

    PubMed Central

    Rahrig, Ryan R.; Leontis, Neocles B.; Zirbel, Craig L.

    2010-01-01

    Motivation: Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the ‘local alignment’ graph. Results: The algorithm is implemented in a program suite and web server called ‘R3D Align’. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments. Availability: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: r-rahrig@onu.edu PMID:20929913

  6. Local alignment of two-base encoded DNA sequence

    PubMed Central

    Homer, Nils; Merriman, Barry; Nelson, Stanley F

    2009-01-01

    Background DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an encoded form, such as the two-base encoding considered here. In order to compare such data to a reference sequence, the data must be decoded into sequence. The decoding is deterministic, but the possibility of measurement errors requires searching among all possible error modes and resulting alignments to achieve an optimal balance of fewer errors versus greater sequence similarity. Results We present an extension of the standard dynamic programming method for local alignment, which simultaneously decodes the data and performs the alignment, maximizing a similarity score based on a weighted combination of errors and edits, and allowing an affine gap penalty. We also present simulations that demonstrate the performance characteristics of our two base encoded alignment method and contrast those with standard DNA sequence alignment under the same conditions. Conclusion The new local alignment algorithm for two-base encoded data has substantial power to properly detect and correct measurement errors while identifying underlying sequence variants, and facilitating genome re-sequencing efforts based on this form of sequence data. PMID:19508732

  7. Matt: local flexibility aids protein multiple structure alignment.

    PubMed

    Menke, Matthew; Berger, Bonnie; Cowen, Lenore

    2008-01-01

    Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geometrically consistent ways. Ye and Godzik have recently suggested that adding geometric flexibility may help better model protein structures in a variety of contexts. We introduce the program Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations. After a dynamic programming assembly guided by these "bent" alignments, geometric consistency is restored in the final step before the alignment is output. Matt is tested against other recent multiple protein structure alignment programs on the popular Homstrad and SABmark benchmark datasets. Matt's global performance is competitive with the other programs on Homstrad, but outperforms the other programs on SABmark, a benchmark of multiple structure alignments of proteins with more distant homology. On both datasets, Matt demonstrates an ability to better align the ends of alpha-helices and beta-strands, an important characteristic of any structure alignment program intended to help construct a structural template library for threading approaches to the inverse protein-folding problem. The related question of whether Matt alignments can be used to distinguish distantly homologous structure pairs from pairs of proteins that are not homologous is also considered. For this purpose, a p-value score based on the length of the common core and average root

  8. Proteins comparison through probabilistic optimal structure local alignment

    PubMed Central

    Micale, Giovanni; Pulvirenti, Alfredo; Giugno, Rosalba; Ferro, Alfredo

    2014-01-01

    Multiple local structure comparison helps to identify common structural motifs or conserved binding sites in 3D structures in distantly related proteins. Since there is no best way to compare structures and evaluate the alignment, a wide variety of techniques and different similarity scoring schemes have been proposed. Existing algorithms usually compute the best superposition of two structures or attempt to solve it as an optimization problem in a simpler setting (e.g., considering contact maps or distance matrices). Here, we present PROPOSAL (PROteins comparison through Probabilistic Optimal Structure local ALignment), a stochastic algorithm based on iterative sampling for multiple local alignment of protein structures. Our method can efficiently find conserved motifs across a set of protein structures. Only the distances between all pairs of residues in the structures are computed. To show the accuracy and the effectiveness of PROPOSAL we tested it on a few families of protein structures. We also compared PROPOSAL with two state-of-the-art tools for pairwise local alignment on a dataset of manually annotated motifs. PROPOSAL is available as a Java 2D standalone application or a command line program at http://ferrolab.dmi.unict.it/proposal/proposal.html. PMID:25228906

  9. Heuristic reusable dynamic programming: efficient updates of local sequence alignment.

    PubMed

    Hong, Changjin; Tewfik, Ahmed H

    2009-01-01

    Recomputation of the previously evaluated similarity results between biological sequences becomes inevitable when researchers realize errors in their sequenced data or when the researchers have to compare nearly similar sequences, e.g., in a family of proteins. We present an efficient scheme for updating local sequence alignments with an affine gap model. In principle, using the previous matching result between two amino acid sequences, we perform a forward-backward alignment to generate heuristic searching bands which are bounded by a set of suboptimal paths. Given a correctly updated sequence, we initially predict a new score of the alignment path for each contour to select the best candidates among them. Then, we run the Smith-Waterman algorithm in this confined space. Furthermore, our heuristic alignment for an updated sequence shows that it can be further accelerated by using reusable dynamic programming (rDP), our prior work. In this study, we successfully validate "relative node tolerance bound" (RNTB) in the pruned searching space. Furthermore, we improve the computational performance by quantifying the successful RNTB tolerance probability and switch to rDP on perturbation-resilient columns only. In our searching space derived by a threshold value of 90 percent of the optimal alignment score, we find that 98.3 percent of contours contain correctly updated paths. We also find that our method consumes only 25.36 percent of the runtime cost of sparse dynamic programming (sDP) method, and to only 2.55 percent of that of a normal dynamic programming with the Smith-Waterman algorithm. PMID:19875856

  10. Local search for the generalized tree alignment problem

    PubMed Central

    2013-01-01

    Background A phylogeny postulates shared ancestry relationships among organisms in the form of a binary tree. Phylogenies attempt to answer an important question posed in biology: what are the ancestor-descendent relationships between organisms? At the core of every biological problem lies a phylogenetic component. The patterns that can be observed in nature are the product of complex interactions, constrained by the template that our ancestors provide. The problem of simultaneous tree and alignment estimation under Maximum Parsimony is known in combinatorial optimization as the Generalized Tree Alignment Problem (GTAP). The GTAP is the Steiner Tree Problem for the sequence edit distance. Like many biologically interesting problems, the GTAP is NP-Hard. Typically the Steiner Tree is presented under the Manhattan or the Hamming distances. Results Experimentally, the accuracy of the GTAP has been subjected to evaluation. Results show that phylogenies selected using the GTAP from unaligned sequences are competitive with the best methods and algorithms available. Here, we implement and explore experimentally existing and new local search heuristics for the GTAP using simulated and real data. Conclusions The methods presented here improve by more than three orders of magnitude in execution time the best local search heuristics existing to date when applied to real data. PMID:23441880

  11. Enhancement of initial equivalency for protein structure alignment based on encoded local structures.

    PubMed

    Hung, Kenneth; Wang, Jui-Chih; Chen, Cheng-Wei; Chuang, Cheng-Long; Tsai, Kun-Nan; Chen, Chung-Ming

    2012-11-01

    Most alignment algorithms find an initial equivalent residue pair followed by an iterative optimization process to explore better near-optimal alignments in the surrounding solution space of the initial alignment. It plays a decisive role in determining the alignment quality since a poor initial alignment may make the final alignment trapped in an undesirable local optimum even with an iterative optimization. We proposed a vector-based alignment algorithm with a new initial alignment approach accounting for local structure features called MIRAGE-align. The new idea is to enhance the quality of the initial alignment based on encoded local structural alphabets to identify the protein structure pair whose sequence identity falls in or below twilight zone. The statistical analysis of alignment quality based on Match Index (MI) and computation time demonstrated that MIRAGE-align algorithm outperformed four previously published algorithms, i.e., the residue-based algorithm (CE), the vector-based algorithm (SSM), TM-align, and Fr-TM-align. MIRAGE-align yields a better estimate of initial solution to enhance the quality of initial alignment and enable the employment of a non-iterative optimization process to achieve a better alignment. PMID:22717522

  12. Skeleton-based human action recognition using multiple sequence alignment

    NASA Astrophysics Data System (ADS)

    Ding, Wenwen; Liu, Kai; Cheng, Fei; Zhang, Jin; Li, YunSong

    2015-05-01

    Human action recognition and analysis is an active research topic in computer vision for many years. This paper presents a method to represent human actions based on trajectories consisting of 3D joint positions. This method first decompose action into a sequence of meaningful atomic actions (actionlets), and then label actionlets with English alphabets according to the Davies-Bouldin index value. Therefore, an action can be represented using a sequence of actionlet symbols, which will preserve the temporal order of occurrence of each of the actionlets. Finally, we employ sequence comparison to classify multiple actions through using string matching algorithms (Needleman-Wunsch). The effectiveness of the proposed method is evaluated on datasets captured by commodity depth cameras. Experiments of the proposed method on three challenging 3D action datasets show promising results.

  13. Conditional alignment random fields for multiple motion sequence alignment.

    PubMed

    Kim, Minyoung

    2013-11-01

    We consider the multiple time-series alignment problem, typically focusing on the task of synchronizing multiple motion videos of the same kind of human activity. Finding an optimal global alignment of multiple sequences is infeasible, while there have been several approximate solutions, including iterative pairwise warping algorithms and variants of hidden Markov models. In this paper, we propose a novel probabilistic model that represents the conditional densities of the latent target sequences which are aligned with the given observed sequences through the hidden alignment variables. By imposing certain constraints on the target sequences at the learning stage, we have a sensible model for multiple alignments that can be learned very efficiently by the EM algorithm. Compared to existing methods, our approach yields more accurate alignment while being more robust to local optima and initial configurations. We demonstrate its efficacy on both synthetic and real-world motion videos including facial emotions and human activities. PMID:24051737

  14. GASOLINE: a Cytoscape app for multiple local alignment of PPI networks

    PubMed Central

    Micale, Giovanni; Continella, Andrea; Ferro, Alfredo; Giugno, Rosalba; Pulvirenti, Alfredo

    2014-01-01

    Comparing protein interaction networks can reveal interesting patterns of interactions for a specific function or process in distantly related species. In this paper we present GASOLINE, a Cytoscape app for multiple local alignments of PPI (protein-protein interaction) networks. The app is based on the homonymous greedy and stochastic algorithm. GASOLINE starts with the identification of sets of similar nodes, called seeds of the alignment. Alignments are then extended in a greedy manner and finally refined. Both the identification of seeds and the extension of alignments are performed through an iterative Gibbs sampling strategy. GASOLINE is a Cytoscape app for computing and visualizing local alignments, without requiring any post-processing operations. GO terms can be easily attached to the aligned proteins for further functional analysis of alignments. GASOLINE can perform the alignment task in few minutes, even for a large number of input networks. PMID:25324964

  15. Citation Matching in Sanskrit Corpora Using Local Alignment

    NASA Astrophysics Data System (ADS)

    Prasad, Abhinandan S.; Rao, Shrisha

    Citation matching is the problem of finding which citation occurs in a given textual corpus. Most existing citation matching work is done on scientific literature. The goal of this paper is to present methods for performing citation matching on Sanskrit texts. Exact matching and approximate matching are the two methods for performing citation matching. The exact matching method checks for exact occurrence of the citation with respect to the textual corpus. Approximate matching is a fuzzy string-matching method which computes a similarity score between an individual line of the textual corpus and the citation. The Smith-Waterman-Gotoh algorithm for local alignment, which is generally used in bioinformatics, is used here for calculating the similarity score. This similarity score is a measure of the closeness between the text and the citation. The exact- and approximate-matching methods are evaluated and compared. The methods presented can be easily applied to corpora in other Indic languages like Kannada, Tamil, etc. The approximate-matching method can in particular be used in the compilation of critical editions and plagiarism detection in a literary work.

  16. DNA Align Editor: DNA Alignment Editor Tool

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The SNPAlignEditor is a DNA sequence alignment editor that runs on Windows platforms. The purpose of the program is to provide an intuitive, user-friendly tool for manual editing of multiple sequence alignments by providing functions for input, editing, and output of nucleotide sequence alignments....

  17. Swarm intelligence in bioinformatics: methods and implementations for discovering patterns of multiple sequences.

    PubMed

    Cui, Zhihua; Zhang, Yi

    2014-02-01

    As a promising and innovative research field, bioinformatics has attracted increasing attention recently. Beneath the enormous number of open problems in this field, one fundamental issue is about the accurate and efficient computational methodology that can deal with tremendous amounts of data. In this paper, we survey some applications of swarm intelligence to discover patterns of multiple sequences. To provide a deep insight, ant colony optimization, particle swarm optimization, artificial bee colony and artificial fish swarm algorithm are selected, and their applications to multiple sequence alignment and motif detecting problem are discussed. PMID:24749453

  18. Alignments of the galaxies in and around the Virgo cluster with the local velocity shear

    SciTech Connect

    Lee, Jounghun; Rey, Soo Chang; Kim, Suk

    2014-08-10

    Observational evidence is presented for the alignment between the cosmic sheet and the principal axis of the velocity shear field at the position of the Virgo cluster. The galaxies in and around the Virgo cluster from the Extended Virgo Cluster Catalog that was recently constructed by Kim et al. are used to determine the direction of the local sheet. The peculiar velocity field reconstructed from the Sloan Digital Sky Survey Data Release 7 is analyzed to estimate the local velocity shear tensor at the Virgo center. Showing first that the minor principal axis of the local velocity shear tensor is almost parallel to the direction of the line of sight, we detect a clear signal of alignment between the positions of the Virgo satellites and the intermediate principal axis of the local velocity shear projected onto the plane of the sky. Furthermore, the dwarf satellites are found to appear more strongly aligned than their normal counterparts, which is interpreted as an indication of the following. (1) The normal satellites and the dwarf satellites fall in the Virgo cluster preferentially along the local filament and the local sheet, respectively. (2) The local filament is aligned with the minor principal axis of the local velocity shear while the local sheet is parallel to the plane spanned by the minor and intermediate principal axes. Our result is consistent with the recent numerical claim that the velocity shear is a good tracer of the cosmic web.

  19. Alignments of the Galaxies in and around the Virgo Cluster with the Local Velocity Shear

    NASA Astrophysics Data System (ADS)

    Lee, Jounghun; Rey, Soo Chang; Kim, Suk

    2014-08-01

    Observational evidence is presented for the alignment between the cosmic sheet and the principal axis of the velocity shear field at the position of the Virgo cluster. The galaxies in and around the Virgo cluster from the Extended Virgo Cluster Catalog that was recently constructed by Kim et al. are used to determine the direction of the local sheet. The peculiar velocity field reconstructed from the Sloan Digital Sky Survey Data Release 7 is analyzed to estimate the local velocity shear tensor at the Virgo center. Showing first that the minor principal axis of the local velocity shear tensor is almost parallel to the direction of the line of sight, we detect a clear signal of alignment between the positions of the Virgo satellites and the intermediate principal axis of the local velocity shear projected onto the plane of the sky. Furthermore, the dwarf satellites are found to appear more strongly aligned than their normal counterparts, which is interpreted as an indication of the following. (1) The normal satellites and the dwarf satellites fall in the Virgo cluster preferentially along the local filament and the local sheet, respectively. (2) The local filament is aligned with the minor principal axis of the local velocity shear while the local sheet is parallel to the plane spanned by the minor and intermediate principal axes. Our result is consistent with the recent numerical claim that the velocity shear is a good tracer of the cosmic web.

  20. SoftSearch: Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations

    PubMed Central

    Hart, Steven N.; Sarangi, Vivekananda; Moore, Raymond; Baheti, Saurabh; Bhavsar, Jaysheel D.; Couch, Fergus J.; Kocher, Jean-Pierre A.

    2013-01-01

    Background Structural variation (SV) represents a significant, yet poorly understood contribution to an individual’s genetic makeup. Advanced next-generation sequencing technologies are widely used to discover such variations, but there is no single detection tool that is considered a community standard. In an attempt to fulfil this need, we developed an algorithm, SoftSearch, for discovering structural variant breakpoints in Illumina paired-end next-generation sequencing data. SoftSearch combines multiple strategies for detecting SV including split-read, discordant read-pair, and unmated pairs. Co-localized split-reads and discordant read pairs are used to refine the breakpoints. Results We developed and validated SoftSearch using real and synthetic datasets. SoftSearch’s key features are 1) not requiring secondary (or exhaustive primary) alignment, 2) portability into established sequencing workflows, and 3) is applicable to any DNA-sequencing experiment (e.g. whole genome, exome, custom capture, etc.). SoftSearch identifies breakpoints from a small number of soft-clipped bases from split reads and a few discordant read-pairs which on their own would not be sufficient to make an SV call. Conclusions We show that SoftSearch can identify more true SVs by combining multiple sequence features. SoftSearch was able to call clinically relevant SVs in the BRCA2 gene not reported by other tools while offering significantly improved overall performance. PMID:24358278

  1. Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

    DOE PAGESBeta

    Daily, Jeffrey A.

    2016-02-10

    Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less

  2. Local-global alignment for finding 3D similarities in protein structures

    DOEpatents

    Zemla, Adam T.

    2011-09-20

    A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

  3. Usp16 regulates kinetochore localization of Plk1 to promote proper chromosome alignment in mitosis

    PubMed Central

    Zhuo, Xiaolong; Guo, Xiao; Zhang, Xiaoyan; Jing, Guihua; Wang, Yao; Chen, Qiang; Jiang, Qing

    2015-01-01

    During the G2 to M phase transition, a portion of mitotic regulator Plk1 localizes to the kinetochores and regulates the initiation of kinetochore–microtubule attachments for proper chromosome alignment. Once kinetochore–microtubule attachment is achieved, this portion of Plk1 is removed from the kinetochores as a result of ubiquitination. However, the crucial molecular mechanism that promotes the localization and the maintenance of Plk1 on the kinetochores until metaphase is still unclear. We report that ubiquitin-specific peptidase 16 (Usp16) plays a key role during this process. Usp16 deubiquitinates Plk1, resulting in an enhanced interaction with kinetochore-localized proteins such as BubR1, and thereby retains Plk1 on the kinetochores to promote proper chromosome alignment in early mitosis. Down-regulation of Usp16 causes increased ubiquitination and decreased kinetochore localization of Plk1. Thus, our data unveil a unique mechanism by which Usp16 promotes the localization and maintenance of Plk1 on the kinetochores for proper chromosome alignment. PMID:26323689

  4. Automatic alignment of multi-temporal images of planetary nebulae using local optimization

    NASA Astrophysics Data System (ADS)

    Kazemzadeh, Farnoud; Hajian, Arsen R.

    2010-08-01

    Automatic alignment of time-separated astronomical images have historically proven to be difficult. The main reason for this difficulty is the amount of sporadic and unpredictable noise associated with astronomical images. A few examples of these effects are: image distortion due to optics, cosmic ray hits, transient background sources (super novae) and various artifact sources associated with the CCD imager itself. In this paper a new automated image registration method is introduced for aligning two time-separated images while minimizing the inherent errors and unpredictabilities. Using local optimization, the two images are aligned when the root mean square of the difference between the two images is minimized. The dataset consists of images of galactic planetary nebulae acquired by the Hubble Space Telescope. The aligned centroids inferred by the suggested method agree with the results from previously aligned images by inspection with high confidence. It is also demonstrated that this method is robust, sufficient, does not require extensive user input and it is highly sensitive to minor adjustments.

  5. Method of Deployment of a Space Tethered System Aligned to the Local Vertical

    NASA Astrophysics Data System (ADS)

    Zakrzhevskii, A. E.

    2016-04-01

    The object of this research is a space tether of two bodies connected by a flexible massless string. The research objective is the development and theoretical justification of a novel approach to the solution of the problem of deployment of the space tether in a circular orbit with its alignment to the local vertical. The approach is based on use of the theorem on the angular momentum change. It allows developing the open-loop control of the tether length that provides desired change of the angular momentum of the tether under the effect of the gravitational torque to the value, which corresponds to the angular momentum of the deployed tether aligned to the local vertical. The given example of application of the approach to a case of deployment of a tether demonstrates the simplicity of use of the method in practice, and also the method of validation of the mathematical model.

  6. Method of Deployment of a Space Tethered System Aligned to the Local Vertical

    NASA Astrophysics Data System (ADS)

    Zakrzhevskii, A. E.

    2016-09-01

    The object of this research is a space tether of two bodies connected by a flexible massless string. The research objective is the development and theoretical justification of a novel approach to the solution of the problem of deployment of the space tether in a circular orbit with its alignment to the local vertical. The approach is based on use of the theorem on the angular momentum change. It allows developing the open-loop control of the tether length that provides desired change of the angular momentum of the tether under the effect of the gravitational torque to the value, which corresponds to the angular momentum of the deployed tether aligned to the local vertical. The given example of application of the approach to a case of deployment of a tether demonstrates the simplicity of use of the method in practice, and also the method of validation of the mathematical model.

  7. A Method for Non-Rigid Face Alignment via Combining Local and Holistic Matching

    PubMed Central

    Yang, Yang; Chen, Zhuo

    2016-01-01

    We propose a method for non-rigid face alignment which only needs a single template, such as using a person’s smile face to match his surprise face. First, in order to be robust to outliers caused by complex geometric deformations, a new local feature matching method called K Patch Pairs (K-PP) is proposed. Specifically, inspired by the state-of-art similarity measure used in template matching, K-PP is to find the mutual K nearest neighbors between two images. A weight matrix is then presented to balance the similarity and the number of local matching. Second, we proposed a modified Lucas-Kanade algorithm combined with local matching constraint to solve the non-rigid face alignment, so that a holistic face representation and local features can be jointly modeled in the object function. Both the flexible ability of local matching and the robust ability of holistic fitting are included in our method. Furthermore, we show that the optimization problem can be efficiently solved by the inverse compositional algorithm. Comparison results with conventional methods demonstrate our superiority in terms of both accuracy and robustness. PMID:27494319

  8. Hole localization, water dissociation mechanisms, and band alignment at aqueous-titania interfaces

    NASA Astrophysics Data System (ADS)

    Lyons, John L.

    Photocatalytic water splitting is a promising method for generating clean energy, but materials that can efficiently act as photocatalysts are scarce. This is in part due to the fact that exposure to water can strongly alter semiconductor surfaces and therefore photocatalyst performance. Many materials are not stable in aqueous environments; in other cases, local changes in structure may occur, affecting energy-level alignment. Even in the simplest case, dynamic fluctuations modify the organization of interface water. Accounting for such effects requires knowledge of the dominant local structural motifs and also accurate semiconductor band-edge positions, making quantitative prediction of energy-level alignments computationally challenging. Here we employ a combined theoretical approach to study the structure, energy alignment, and hole localization at aqueous-titania interfaces. We calculate the explicit aqueous-semiconductor interface using ab initio molecular dynamics, which provides the fluctuating atomic structure, the extent of water dissociation, and the resulting electrostatic potential. For both anatase and rutile TiO2 we observe spontaneous water dissociation and re-association events that occur via distinct mechanisms. We also find a higher-density water layer occurring on anatase. In both cases, we find that the second monolayer of water plays a crucial role in controlling the extent of water dissociation. Using hybrid functional calculations, we then investigate the propensity for dissociated waters to stabilize photo-excited carriers, and compare the results of rutile and anatase aqueous interfaces. Finally, we use the GW approach from many-body perturbation theory to obtain the position of semiconductor band edges relative to the occupied 1b1 level and thus the redox levels of water, and examine how local structural modifications affect these offsets. This work was performed in collaboration with N. Kharche, M. Z. Ertem, J. T. Muckerman, and M. S

  9. Finite-temperature local protein sequence alignment: percolation and free-energy distribution.

    PubMed

    Wolfsheimer, S; Melchert, O; Hartmann, A K

    2009-12-01

    Sequence alignment is a tool in bioinformatics that is used to find homological relationships in large molecular databases. It can be mapped on the physical model of directed polymers in random media. We consider the finite-temperature version of local sequence alignment for proteins and study the transition between the linear phase and the biologically relevant logarithmic phase, where the free energy grows linearly or logarithmically with the sequence length. By means of numerical simulations and finite-size-scaling analysis, we determine the phase diagram in the plane that is spanned by the gap costs and the temperature. We use the most frequently used parameter set for protein alignment. The critical exponents that describe the parameter-driven transition are found to be explicitly temperature dependent. Furthermore, we study the shape of the (free-) energy distribution close to the transition by rare-event simulations down to probabilities on the order 10(-64). It is well known that in the logarithmic region, the optimal score distribution (T=0) is described by a modified Gumbel distribution. We confirm that this also applies for the free-energy distribution (T>0). However, in the linear phase, the distribution crosses over to a modified Gaussian distribution. PMID:20365196

  10. Co-Orientation: Quantifying Simultaneous Co-Localization and Orientational Alignment of Filaments in Light Microscopy

    PubMed Central

    Manders, Erik M. M.; Jalink, Kees; Stallinga, Sjoerd; Rieger, Bernd

    2015-01-01

    Co-localization analysis is a widely used tool to seek evidence for functional interactions between molecules in different color channels in microscopic images. Here we extend the basic co-localization analysis by including the orientations of the structures on which the molecules reside. We refer to the combination of co-localization of molecules and orientational alignment of the structures on which they reside as co-orientation. Because the orientation varies with the length scale at which it is evaluated, we consider this scale as a separate informative dimension in the analysis. Additionally we introduce a data driven method for testing the statistical significance of the co-orientation and provide a method for visualizing the local co-orientation strength in images. We demonstrate our methods on simulated localization microscopy data of filamentous structures, as well as experimental images of similar structures acquired with localization microscopy in different color channels. We also show that in cultured primary HUVEC endothelial cells, filaments of the intermediate filament vimentin run close to and parallel with microtubuli. In contrast, no co-orientation was found between keratin and actin filaments. Co-orientation between vimentin and tubulin was also observed in an endothelial cell line, albeit to a lesser extent, but not in 3T3 fibroblasts. These data therefore suggest that microtubuli functionally interact with the vimentin network in a cell-type specific manner. PMID:26161965

  11. Mapping local orientation of aligned fibrous scatterers for cancerous tissues using backscattering Mueller matrix imaging

    NASA Astrophysics Data System (ADS)

    He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Liu, Shaoxiong; Guo, Yihong; Wu, Jian; He, Yonghong; Ma, Hui

    2014-10-01

    Polarization measurements are sensitive to the microstructure of tissues and can be used to detect pathological changes. Many tissues contain anisotropic fibrous structures. We obtain the local orientation of aligned fibrous scatterers using different groups of the backscattering Mueller matrix elements. Experiments on concentrically well-aligned silk fibers and unstained human papillary thyroid carcinoma tissues show that the m22, m33, m23, and m32 elements have better contrast but higher degeneracy for the extraction of orientation angles. The m12 and m13 elements show lower contrast, but allow us to determine the orientation angle for the fibrous scatterers along all directions. Moreover, Monte Carlo simulations based on the sphere-cylinder scattering model indicate that the oblique incidence of the illumination beam introduces some errors in the orientation angles obtained by both methods. Mapping the local orientation of anisotropic tissues may not only provide information on pathological changes, but can also give new leads to reduce the orientation dependence of polarization measurements.

  12. Understanding the nanoscale local buckling behavior of vertically aligned MWCNT arrays with van der Waals interactions.

    PubMed

    Li, Yupeng; Kim, Hyung-ick; Wei, Bingqing; Kang, Junmo; Choi, Jae-boong; Nam, Jae-Do; Suhr, Jonghwan

    2015-09-14

    The local buckling behavior of vertically aligned carbon nanotubes (VACNTs) has been investigated and interpreted in the view of a collective nanotube response by taking van der Waals interactions into account. To the best of our knowledge, this is the first report on the case of collective VACNT behavior regarding van der Waals force among nanotubes as a lateral support effect during the buckling process. The local buckling propagation and development of VACNTs were experimentally observed and theoretically analyzed by employing finite element modeling with lateral support from van der Waals interactions among nanotubes. Both experimental and theoretical analyses show that VACNTs buckled in the bottom region with many short waves and almost identical wavelengths, indicating a high mode buckling. Furthermore, the propagation and development mechanism of buckling waves follow the wave damping effect. PMID:26242771

  13. Understanding the nanoscale local buckling behavior of vertically aligned MWCNT arrays with van der Waals interactions

    NASA Astrophysics Data System (ADS)

    Li, Yupeng; Kim, Hyung-Ick; Wei, Bingqing; Kang, Junmo; Choi, Jae-Boong; Nam, Jae-Do; Suhr, Jonghwan

    2015-08-01

    The local buckling behavior of vertically aligned carbon nanotubes (VACNTs) has been investigated and interpreted in the view of a collective nanotube response by taking van der Waals interactions into account. To the best of our knowledge, this is the first report on the case of collective VACNT behavior regarding van der Waals force among nanotubes as a lateral support effect during the buckling process. The local buckling propagation and development of VACNTs were experimentally observed and theoretically analyzed by employing finite element modeling with lateral support from van der Waals interactions among nanotubes. Both experimental and theoretical analyses show that VACNTs buckled in the bottom region with many short waves and almost identical wavelengths, indicating a high mode buckling. Furthermore, the propagation and development mechanism of buckling waves follow the wave damping effect.The local buckling behavior of vertically aligned carbon nanotubes (VACNTs) has been investigated and interpreted in the view of a collective nanotube response by taking van der Waals interactions into account. To the best of our knowledge, this is the first report on the case of collective VACNT behavior regarding van der Waals force among nanotubes as a lateral support effect during the buckling process. The local buckling propagation and development of VACNTs were experimentally observed and theoretically analyzed by employing finite element modeling with lateral support from van der Waals interactions among nanotubes. Both experimental and theoretical analyses show that VACNTs buckled in the bottom region with many short waves and almost identical wavelengths, indicating a high mode buckling. Furthermore, the propagation and development mechanism of buckling waves follow the wave damping effect. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03581c

  14. Equatorial longitude and local time variations of topside magnetic field-aligned ion drifts at solar minimum

    NASA Astrophysics Data System (ADS)

    Burrell, A. G.; Heelis, R. A.; Stoneback, R. A.

    2012-04-01

    In the topside ionosphere, the high mobility of the plasma along the magnetic field allows field-aligned ion drifts to occur readily as a result of field-aligned gravitational forces, collisional forces, or pressure gradients. Therefore, variations in the field-aligned ion drifts can be used to explore the influence of thermospheric, electrodynamic, and chemical processes on the ionosphere. Longitude and local time variations in the field-aligned ion drifts near the magnetic equator are presented using observations from the Coupled Ion Neutral Dynamics Investigation on board the Communications/Navigation Outage Forecast System satellite. These observations were obtained during the period of extremely low solar activity present in 2008 and 2009, allowing the seasonal, local time, and longitudinal variations to reveal the relative importance of the processes responsible for topside field-aligned plasma drifts during solar minimum. This investigation found that the low-altitude winds and tides, the net ionization or loss, and the meridional E×B drift were all influential in creating longitudinal and local time variations in the field-aligned drift, though the strength of the influence seen by each driver was found to vary with season, local time, and longitude.

  15. Java bioinformatics analysis web services for multiple sequence alignment—JABAWS:MSA

    PubMed Central

    Troshin, Peter V.; Procter, James B.; Barton, Geoffrey J.

    2011-01-01

    Summary: JABAWS is a web services framework that simplifies the deployment of web services for bioinformatics. JABAWS:MSA provides services for five multiple sequence alignment (MSA) methods (Probcons, T-coffee, Muscle, Mafft and ClustalW), and is the system employed by the Jalview multiple sequence analysis workbench since version 2.6. A fully functional, easy to set up server is provided as a Virtual Appliance (VA), which can be run on most operating systems that support a virtualization environment such as VMware or Oracle VirtualBox. JABAWS is also distributed as a Web Application aRchive (WAR) and can be configured to run on a single computer and/or a cluster managed by Grid Engine, LSF or other queuing systems that support DRMAA. JABAWS:MSA provides clients full access to each application's parameters, allows administrators to specify named parameter preset combinations and execution limits for each application through simple configuration files. The JABAWS command-line client allows integration of JABAWS services into conventional scripts. Availability and Implementation: JABAWS is made freely available under the Apache 2 license and can be obtained from: http://www.compbio.dundee.ac.uk/jabaws. Contact: g.j.barton@dundee.ac.uk PMID:21593132

  16. Local time resolved dynamics of field-aligned currents and their response to solar wind variability

    NASA Astrophysics Data System (ADS)

    He, Maosheng; Vogt, Joachim; Lühr, Hermann; Sorbalo, Eugen

    2014-07-01

    Using 10 years of CHAMP measurements condensed into the empirical model of field-aligned currents through empirical orthogonal function analysis, the dynamics of field-aligned currents (FACs) is modeled and studied in separate magnetic local time (MLT) sectors. We investigate the distributions of FAC intensity and latitude and evaluate their predictability in terms of geospace parameters which are ranked according to their relative importance measured by a multivariate regression procedure. The response time to changes in solar wind variables is studied in detail and found to be much shorter for dayside FACs than on the nightside (15-25 min versus 35-95 min). Furthermore, dayside FACs can be parameterized more accurately: R2 values maximize greater than 0.7 for FAC latitude and greater than 0.3 for FAC intensity, whereas the corresponding values on the nightside are smaller than 0.3 and 0.15, respectively. The results support the separation between directly driven coupling processes acting on the dayside and unloading processes controlling the nightside. In addition, the MLT-resolved standardized regression coefficients suggest that (1) FAC latitude is affected most significantly by the transpolar potential, substorm evolution, solar activity as represented by the F10.7 index and its square, and the dipole tilt; (2) Region-1/2 current intensity is controlled most efficiently by substorm evolution, IMF Bz and IMF By; and (3) cusp current intensity is influenced by conductivity, IMF By and their cross item.

  17. Global classical solutions of the Vlasov–Fokker–Planck equation with local alignment forces

    NASA Astrophysics Data System (ADS)

    Choi, Young-Pil

    2016-07-01

    In this paper, we are concerned with the global well-posedness and time-asymptotic decay of the Vlasov–Fokker–Planck equation with local alignment forces. The equation can be formally derived from an agent-based model for self-organized dynamics called the Motsch–Tadmor model with noises. We present the global existence and uniqueness of classical solutions to the equation around the global Maxwellian in the whole space. For the large-time behavior, we show the algebraic decay rate of solutions towards the equilibrium under suitable assumptions on the initial data. We also remark that the rate of convergence is exponential when the spatial domain is periodic. The main methods used in this paper are the classical energy estimates combined with hyperbolic–parabolic dissipation arguments.

  18. Ultra-large alignments using phylogeny-aware profiles.

    PubMed

    Nguyen, Nam-Phuong D; Mirarab, Siavash; Kumar, Keerthana; Warnow, Tandy

    2015-01-01

    Many biological questions, including the estimation of deep evolutionary histories and the detection of remote homology between protein sequences, rely upon multiple sequence alignments and phylogenetic trees of large datasets. However, accurate large-scale multiple sequence alignment is very difficult, especially when the dataset contains fragmentary sequences. We present UPP, a multiple sequence alignment method that uses a new machine learning technique, the ensemble of hidden Markov models, which we propose here. UPP produces highly accurate alignments for both nucleotide and amino acid sequences, even on ultra-large datasets or datasets containing fragmentary sequences. UPP is available at https://github.com/smirarab/sepp . PMID:26076734

  19. Efficient Constrained Local Model Fitting for Non-Rigid Face Alignment

    PubMed Central

    Wang, Yang; Cox, Mark; Sridharan, Sridha; Cohn, Jeffery F.

    2009-01-01

    Active appearance models (AAMs) have demonstrated great utility when being employed for non-rigid face alignment/tracking. The “simultaneous” algorithm for fitting an AAM achieves good non-rigid face registration performance, but has poor real time performance (2-3 fps). The “project-out” algorithm for fitting an AAM achieves faster than real time performance (> 200 fps) but suffers from poor generic alignment performance. In this paper we introduce an extension to a discriminative method for non-rigid face registration/tracking referred to as a constrained local model (CLM). Our proposed method is able to achieve superior performance to the “simultaneous” AAM algorithm along with real time fitting speeds (35 fps). We improve upon the canonical CLM formulation, to gain this performance, in a number of ways by employing: (i) linear SVMs as patch-experts, (ii) a simplified optimization criteria, and (iii) a composite rather than additive warp update step. Most notably, our simplified optimization criteria for fitting the CLM divides the problem of finding a single complex registration/warp displacement into that of finding N simple warp displacements. From these N simple warp displacements, a single complex warp displacement is estimated using a weighted least-squares constraint. Another major advantage of this simplified optimization lends from its ability to be parallelized, a step which we also theoretically explore in this paper. We refer to our approach for fitting the CLM as the “exhaustive local search” (ELS) algorithm. Experiments were conducted on the CMU Multi-PIE database. PMID:20046797

  20. Global and local alignments in HIV/AIDS prevention trainings: a case study from Burkina Faso.

    PubMed

    Drescher, Martina

    2007-01-01

    This article presents a linguistic analysis of data from an ongoing research project exploring HIV/AIDS education in West African Burkina Faso. I argue that we can identify different, sometimes even competing, discourses about the disease in prevention interactions. Thus, communication about HIV/AIDS in Burkina Faso--and probably in most of the Sub-Saharan countries--might be characterized by what I will call, with reference to Bakhtin, discursive heteroglossia. There is clear evidence of such discursive heteroglossia, that is, the participants' alignment to local and global HIV discourses, deployed in the communication of health workers. In my analysis of peer educators training sessions, I draw on theoretical and methodological principles from discourse analysis and interactional linguistics. I focus on the linguistic devices and conversational strategies the participants use to indicate the relevance of the local or the global discourses. Three particular devices--namely, metaphors, epistemic and evidential markers, and word explanations--will be examined in a more detailed way. I will also show how the local and the global interweave at different levels of prevention discourse. PMID:17714039

  1. Effect of preconditioning and stress relaxation on local collagen fiber re-alignment: inhomogeneous properties of rat supraspinatus tendon.

    PubMed

    Miller, Kristin S; Edelstein, Lena; Connizzo, Brianne K; Soslowsky, Louis J

    2012-03-01

    Repeatedly and consistently measuring the mechanical properties of tendon is important but presents a challenge. Preconditioning can provide tendons with a consistent loading history to make comparisons between groups from mechanical testing experiments. However, the specific mechanisms occurring during preconditioning are unknown. Previous studies have suggested that microstructural changes, such as collagen fiber re-alignment, may be a result of preconditioning. Local collagen fiber re-alignment is quantified throughout tensile mechanical testing using a testing system integrated with a polarized light setup, consisting of a backlight, 90 deg-offset rotating polarizer sheets on each side of the test sample, and a digital camera, in a rat supraspinatus tendon model, and corresponding mechanical properties are measured. Local circular variance values are compared throughout the mechanical test to determine if and where collagen fiber re-alignment occurred. The inhomogeneity of the tendon is examined by comparing local circular variance values, optical moduli and optical transition strain values. Although the largest amount of collagen fiber re-alignment was found during preconditioning, significant re-alignment was also demonstrated in the toe and linear regions of the mechanical test. No significant changes in re-alignment were seen during stress relaxation. The insertion site of the supraspinatus tendon demonstrated a lower linear modulus and a more disorganized collagen fiber distribution throughout all mechanical testing points compared to the tendon midsubstance. This study identified a correlation between collagen fiber re-alignment and preconditioning and suggests that collagen fiber re-alignment may be a potential mechanism of preconditioning and merits further investigation. In particular, the conditions necessary for collagen fibers to re-orient away from the direction of loading and the dependency of collagen reorganization on its initial distribution

  2. GraphClust: alignment-free structural clustering of local RNA secondary structures

    PubMed Central

    Rose, Dominic; Backofen, Rolf

    2012-01-01

    Motivation: Clustering according to sequence–structure similarity has now become a generally accepted scheme for ncRNA annotation. Its application to complete genomic sequences as well as whole transcriptomes is therefore desirable but hindered by extremely high computational costs. Results: We present a novel linear-time, alignment-free method for comparing and clustering RNAs according to sequence and structure. The approach scales to datasets of hundreds of thousands of sequences. The quality of the retrieved clusters has been benchmarked against known ncRNA datasets and is comparable to state-of-the-art sequence–structure methods although achieving speedups of several orders of magnitude. A selection of applications aiming at the detection of novel structural ncRNAs are presented. Exemplarily, we predicted local structural elements specific to lincRNAs likely functionally associating involved transcripts to vital processes of the human nervous system. In total, we predicted 349 local structural RNA elements. Availability: The GraphClust pipeline is available on request. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22689765

  3. Angular and local spectroscopic analysis to probe the vertical alignment of N-doped well-separated carbon nanotubes.

    PubMed

    Minea, T M; Bouchet-Fabre, B; Lazar, S; Point, S; Zandbergen, H W

    2006-08-17

    Vertically aligned well-separated N-doped multiwalled carbon nanotubes (CNTs) were grown on a silicon substrate by plasma enhanced chemical vapor deposition (PECVD). Angular near-edge X-ray absorption fine structure (NEXAFS) was used to investigate the vertical alignment of as-grown CNTs. In addition, both individual tubes and tube bundles were characterized by high-resolution electron energy loss spectroscopy (HREELS). Simultaneous analysis of both spectroscopic techniques provides information on chemical environment, orbital orientation between carbon and heteroatoms, and local curvature effects. We demonstrate the utility of NEXAFS as an in situ probe of CNTs. PMID:16898707

  4. Interim Report on Multiple Sequence Alignments and TaqMan Signature Mapping to Phylogenetic Trees

    SciTech Connect

    Gardner, S; Jaing, C

    2012-03-27

    The goal of this project is to develop forensic genotyping assays for select agent viruses, addressing a significant capability gap for the viral bioforensics and law enforcement community. We used a multipronged approach combining bioinformatics analysis, PCR-enriched samples, microarrays and TaqMan assays to develop high resolution and cost effective genotyping methods for strain level forensic discrimination of viruses. We have leveraged substantial experience and efficiency gained through year 1 on software development, SNP discovery, TaqMan signature design and phylogenetic signature mapping to scale up the development of forensics signatures in year 2. In this report, we have summarized the Taqman signature development for South American hemorrhagic fever viruses, tick-borne encephalitis viruses and henipaviruses, Old World Arenaviruses, filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus and Japanese encephalitis virus.

  5. Foundations of statistical methods for multiple sequence alignment and structure prediction

    SciTech Connect

    Lawrence, C.

    1995-12-31

    Statistical algorithms have proven to be useful in computational molecular biology. Many statistical problems are most easily addressed by pretending that critical missing data are available. For some problems statistical inference in facilitated by creating a set of latent variables, none of whose variables are observed. A key observation is that conditional probabilities for the values of the missing data can be inferred by application of Bayes theorem to the observed data. The statistical framework described in this paper employs Boltzmann like models, permutated data likelihood, EM, and Gibbs sampler algorithms. This tutorial reviews the common statistical framework behind all of these algorithms largely in tabular or graphical terms, illustrates its application, and describes the biological underpinnings of the models used.

  6. Combining Multiple Pairwise Structure-based Alignments

    SciTech Connect

    2014-11-12

    CombAlign is a new Python code that generates a gapped, one-to-many, multiple structure-based sequence alignment(MSSA) given a set of pairwise structure-based alignments. In order to better define regions of similarity among related protein structures, it is useful to detect the residue-residue correspondences among a set of pairwise structure alignments. Few codes exist for constructing a one-to-many, multiple sequence alignment derived from a set of structure alignments, and we perceived a need for creating a new tool for combing pairwise structure alignments that would allow for insertion of gaps in the reference structure.

  7. Local extracellular matrix alignment directs cellular protrusion dynamics and migration through Rac1 and FAK.

    PubMed

    Carey, Shawn P; Goldblatt, Zachary E; Martin, Karen E; Romero, Bethsabe; Williams, Rebecca M; Reinhart-King, Cynthia A

    2016-08-01

    Cell migration within 3D interstitial microenvironments is sensitive to extracellular matrix (ECM) properties, but the mechanisms that regulate migration guidance by 3D matrix features remain unclear. To examine the mechanisms underlying the cell migration response to aligned ECM, which is prevalent at the tumor-stroma interface, we utilized time-lapse microscopy to compare the behavior of MDA-MB-231 breast adenocarcinoma cells within randomly organized and well-aligned 3D collagen ECM. We developed a novel experimental system in which cellular morphodynamics during initial 3D cell spreading served as a reductionist model for the complex process of matrix-directed 3D cell migration. Using this approach, we found that ECM alignment induced spatial anisotropy of cells' matrix probing by promoting protrusion frequency, persistence, and lengthening along the alignment axis and suppressing protrusion dynamics orthogonal to alignment. Preference for on-axis behaviors was dependent upon FAK and Rac1 signaling and translated across length and time scales such that cells within aligned ECM exhibited accelerated elongation, front-rear polarization, and migration relative to cells in random ECM. Together, these findings indicate that adhesive and protrusive signaling allow cells to respond to coordinated physical cues in the ECM, promoting migration efficiency and cell migration guidance by 3D matrix structure. PMID:27384462

  8. Investigation of terpene diversification across multiple sequenced plant genomes.

    PubMed

    Boutanaev, Alexander M; Moses, Tessa; Zi, Jiachen; Nelson, David R; Mugford, Sam T; Peters, Reuben J; Osbourn, Anne

    2015-01-01

    Plants produce an array of specialized metabolites, including chemicals that are important as medicines, flavors, fragrances, pigments and insecticides. The vast majority of this metabolic diversity is untapped. Here we take a systematic approach toward dissecting genetic components of plant specialized metabolism. Focusing on the terpenes, the largest class of plant natural products, we investigate the basis of terpene diversity through analysis of multiple sequenced plant genomes. The primary drivers of terpene diversification are terpenoid synthase (TS) "signature" enzymes (which generate scaffold diversity), and cytochromes P450 (CYPs), which modify and further diversify these scaffolds, so paving the way for further downstream modifications. Our systematic search of sequenced plant genomes for all TS and CYP genes reveals that distinct TS/CYP gene pairs are found together far more commonly than would be expected by chance, and that certain TS/CYP pairings predominate, providing signals for key events that are likely to have shaped terpene diversity. We recover TS/CYP gene pairs for previously characterized terpene metabolic gene clusters and demonstrate new functional pairing of TSs and CYPs within previously uncharacterized clusters. Unexpectedly, we find evidence for different mechanisms of pathway assembly in eudicots and monocots; in the former, microsyntenic blocks of TS/CYP gene pairs duplicate and provide templates for the evolution of new pathways, whereas in the latter, new pathways arise by mixing and matching of individual TS and CYP genes through dynamic genome rearrangements. This is, to our knowledge, the first documented observation of the unique pattern of TS and CYP assembly in eudicots and monocots. PMID:25502595

  9. Investigation of terpene diversification across multiple sequenced plant genomes

    PubMed Central

    Boutanaev, Alexander M.; Moses, Tessa; Zi, Jiachen; Nelson, David R.; Mugford, Sam T.; Peters, Reuben J.; Osbourn, Anne

    2015-01-01

    Plants produce an array of specialized metabolites, including chemicals that are important as medicines, flavors, fragrances, pigments and insecticides. The vast majority of this metabolic diversity is untapped. Here we take a systematic approach toward dissecting genetic components of plant specialized metabolism. Focusing on the terpenes, the largest class of plant natural products, we investigate the basis of terpene diversity through analysis of multiple sequenced plant genomes. The primary drivers of terpene diversification are terpenoid synthase (TS) “signature” enzymes (which generate scaffold diversity), and cytochromes P450 (CYPs), which modify and further diversify these scaffolds, so paving the way for further downstream modifications. Our systematic search of sequenced plant genomes for all TS and CYP genes reveals that distinct TS/CYP gene pairs are found together far more commonly than would be expected by chance, and that certain TS/CYP pairings predominate, providing signals for key events that are likely to have shaped terpene diversity. We recover TS/CYP gene pairs for previously characterized terpene metabolic gene clusters and demonstrate new functional pairing of TSs and CYPs within previously uncharacterized clusters. Unexpectedly, we find evidence for different mechanisms of pathway assembly in eudicots and monocots; in the former, microsyntenic blocks of TS/CYP gene pairs duplicate and provide templates for the evolution of new pathways, whereas in the latter, new pathways arise by mixing and matching of individual TS and CYP genes through dynamic genome rearrangements. This is, to our knowledge, the first documented observation of the unique pattern of TS and CYP assembly in eudicots and monocots. PMID:25502595

  10. Alignment of Red-Sequence Cluster Dwarf Galaxies: From the Frontier Fields to the Local Universe

    NASA Astrophysics Data System (ADS)

    Barkhouse, Wayne Alan; Archer, Haylee; Burgad, Jaford; Foote, Gregory; Rude, Cody; Lopez-Cruz, Omar

    2015-08-01

    Galaxy clusters are the largest virialized structures in the universe. Due to their high density and mass, they are an excellent laboratory for studying the environmental effects on galaxy evolution. Numerical simulations have predicted that tidal torques acting on dwarf galaxies as they fall into the cluster environment will cause the major axis of the galaxies to align with their radial position vector (a line that extends from the cluster center to the galaxy's center). We have undertaken a study to measure the redshift evolution of the alignment of red-sequence cluster dwarf galaxies based on a sample of 57 low-redshift Abell clusters imaged at KPNO using the 0.9-meter telescope, and 64 clusters from the WINGS dataset. To supplement our low-redshift sample, we have included galaxies selected from the Hubble Space Telescope Frontier fields. Leveraging the HST data allows us to look for evolutionary changes in the alignment of red-sequence cluster dwarf galaxies over a redshift range of 0 < z < 0.35. The alignment of the major axis of the dwarf galaxies is measured by fitting a Sersic function to each red-sequence galaxy using GALFIT. The quality of each model is checked visually after subtracting the model from the galaxy. The cluster sample is then combined by scaling each cluster by r200. We present our preliminary results based on the alignment of the red-sequence dwarf galaxies with: 1) the major axis of the brightest cluster galaxy, 2) the major axis of the cluster defined by the position of cluster members, and 3) a radius vector pointing from the cluster center to individual dwarf galaxies. Our combined cluster sample is sub-divided into different radial regions and redshift bins.

  11. HBLAST: Parallelised sequence similarity--A Hadoop MapReducable basic local alignment search tool.

    PubMed

    O'Driscoll, Aisling; Belogrudov, Vladislav; Carroll, John; Kropp, Kai; Walsh, Paul; Ghazal, Peter; Sleator, Roy D

    2015-04-01

    The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function. As such, parallelised solutions have been proposed but many exhibit scalability limitations and are incapable of effectively processing "Big Data" - the name attributed to datasets that are extremely large, complex and require rapid processing. The Hadoop framework, comprised of distributed storage and a parallelised programming framework known as MapReduce, is specifically designed to work with such datasets but it is not trivial to efficiently redesign and implement bioinformatics algorithms according to this paradigm. The parallelisation strategy of "divide and conquer" for alignment algorithms can be applied to both data sets and input query sequences. However, scalability is still an issue due to memory constraints or large databases, with very large database segmentation leading to additional performance decline. Herein, we present Hadoop Blast (HBlast), a parallelised BLAST algorithm that proposes a flexible method to partition both databases and input query sequences using "virtual partitioning". HBlast presents improved scalability over existing solutions and well balanced computational work load while keeping database segmentation and recompilation to a minimum. Enhanced BLAST search performance on cheap memory constrained hardware has significant implications for in field clinical diagnostic testing; enabling faster and more accurate identification of pathogenic DNA in human blood or tissue samples. PMID:25625550

  12. An Analysis of State and Local Alignment of Teacher Evaluation in Maryland

    ERIC Educational Resources Information Center

    Peterson, Serene N.

    2014-01-01

    This study explored the components of Maryland's newly-implemented teacher evaluation framework and compared state requirements with evaluations to three local school systems' evaluation procedures. The study sought to investigate the relationship between three evaluation protocols in comparison to the state requirements. Three local school…

  13. CSA: An efficient algorithm to improve circular DNA multiple alignment

    PubMed Central

    Fernandes, Francisco; Pereira, Luísa; Freitas, Ana T

    2009-01-01

    Background The comparison of homologous sequences from different species is an essential approach to reconstruct the evolutionary history of species and of the genes they harbour in their genomes. Several complete mitochondrial and nuclear genomes are now available, increasing the importance of using multiple sequence alignment algorithms in comparative genomics. MtDNA has long been used in phylogenetic analysis and errors in the alignments can lead to errors in the interpretation of evolutionary information. Although a large number of multiple sequence alignment algorithms have been proposed to date, they all deal with linear DNA and cannot handle directly circular DNA. Researchers interested in aligning circular DNA sequences must first rotate them to the "right" place using an essentially manual process, before they can use multiple sequence alignment tools. Results In this paper we propose an efficient algorithm that identifies the most interesting region to cut circular genomes in order to improve phylogenetic analysis when using standard multiple sequence alignment algorithms. This algorithm identifies the largest chain of non-repeated longest subsequences common to a set of circular mitochondrial DNA sequences. All the sequences are then rotated and made linear for multiple alignment purposes. To evaluate the effectiveness of this new tool, three different sets of mitochondrial DNA sequences were considered. Other tests considering randomly rotated sequences were also performed. The software package Arlequin was used to evaluate the standard genetic measures of the alignments obtained with and without the use of the CSA algorithm with two well known multiple alignment algorithms, the CLUSTALW and the MAVID tools, and also the visualization tool SinicView. Conclusion The results show that a circularization and rotation pre-processing step significantly improves the efficiency of public available multiple sequence alignment algorithms when used in the

  14. Reconstructing DNA copy number by joint segmentation of multiple sequences

    PubMed Central

    2012-01-01

    Background Variations in DNA copy number carry information on the modalities of genome evolution and mis-regulation of DNA replication in cancer cells. Their study can help localize tumor suppressor genes, distinguish different populations of cancerous cells, and identify genomic variations responsible for disease phenotypes. A number of different high throughput technologies can be used to identify copy number variable sites, and the literature documents multiple effective algorithms. We focus here on the specific problem of detecting regions where variation in copy number is relatively common in the sample at hand. This problem encompasses the cases of copy number polymorphisms, related samples, technical replicates, and cancerous sub-populations from the same individual. Results We present a segmentation method named generalized fused lasso (GFL) to reconstruct copy number variant regions. GFL is based on penalized estimation and is capable of processing multiple signals jointly. Our approach is computationally very attractive and leads to sensitivity and specificity levels comparable to those of state-of-the-art specialized methodologies. We illustrate its applicability with simulated and real data sets. Conclusions The flexibility of our framework makes it applicable to data obtained with a wide range of technology. Its versatility and speed make GFL particularly useful in the initial screening stages of large data sets. PMID:22897923

  15. Robust Eye Center Localization through Face Alignment and Invariant Isocentric Patterns

    PubMed Central

    Teng, Dongdong; Chen, Dihu; Tan, Hongzhou

    2015-01-01

    The localization of eye centers is a very useful cue for numerous applications like face recognition, facial expression recognition, and the early screening of neurological pathologies. Several methods relying on available light for accurate eye-center localization have been exploited. However, despite the considerable improvements that eye-center localization systems have undergone in recent years, only few of these developments deal with the challenges posed by the profile (non-frontal face). In this paper, we first use the explicit shape regression method to obtain the rough location of the eye centers. Because this method extracts global information from the human face, it is robust against any changes in the eye region. We exploit this robustness and utilize it as a constraint. To locate the eye centers accurately, we employ isophote curvature features, the accuracy of which has been demonstrated in a previous study. By applying these features, we obtain a series of eye-center locations which are candidates for the actual position of the eye-center. Among these locations, the estimated locations which minimize the reconstruction error between the two methods mentioned above are taken as the closest approximation for the eye centers locations. Therefore, we combine explicit shape regression and isophote curvature feature analysis to achieve robustness and accuracy, respectively. In practical experiments, we use BioID and FERET datasets to test our approach to obtaining an accurate eye-center location while retaining robustness against changes in scale and pose. In addition, we apply our method to non-frontal faces to test its robustness and accuracy, which are essential in gaze estimation but have seldom been mentioned in previous works. Through extensive experimentation, we show that the proposed method can achieve a significant improvement in accuracy and robustness over state-of-the-art techniques, with our method ranking second in terms of accuracy

  16. Combining Multiple Pairwise Structure-based Alignments

    Energy Science and Technology Software Center (ESTSC)

    2014-11-12

    CombAlign is a new Python code that generates a gapped, one-to-many, multiple structure-based sequence alignment(MSSA) given a set of pairwise structure-based alignments. In order to better define regions of similarity among related protein structures, it is useful to detect the residue-residue correspondences among a set of pairwise structure alignments. Few codes exist for constructing a one-to-many, multiple sequence alignment derived from a set of structure alignments, and we perceived a need for creating a newmore » tool for combing pairwise structure alignments that would allow for insertion of gaps in the reference structure.« less

  17. Multiple alignment using hidden Markov models

    SciTech Connect

    Eddy, S.R.

    1995-12-31

    A simulated annealing method is described for training hidden Markov models and producing multiple sequence alignments from initially unaligned protein or DNA sequences. Simulated annealing in turn uses a dynamic programming algorithm for correctly sampling suboptimal multiple alignments according to their probability and a Boltzmann temperature factor. The quality of simulated annealing alignments is evaluated on structural alignments of ten different protein families, and compared to the performance of other HMM training methods and the ClustalW program. Simulated annealing is better able to find near-global optima in the multiple alignment probability landscape than the other tested HMM training methods. Neither ClustalW nor simulated annealing produce consistently better alignments compared to each other. Examination of the specific cases in which ClustalW outperforms simulated annealing, and vice versa, provides insight into the strengths and weaknesses of current hidden Maxkov model approaches.

  18. SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.

    PubMed

    Jessen, Leon Eyrich; Hoof, Ilka; Lund, Ole; Nielsen, Morten

    2013-07-01

    Identifying which mutation(s) within a given genotype is responsible for an observable phenotype is important in many aspects of molecular biology. Here, we present SigniSite, an online application for subgroup-free residue-level genotype-phenotype correlation. In contrast to similar methods, SigniSite does not require any pre-definition of subgroups or binary classification. Input is a set of protein sequences where each sequence has an associated real number, quantifying a given phenotype. SigniSite will then identify which amino acid residues are significantly associated with the data set phenotype. As output, SigniSite displays a sequence logo, depicting the strength of the phenotype association of each residue and a heat-map identifying 'hot' or 'cold' regions. SigniSite was benchmarked against SPEER, a state-of-the-art method for the prediction of specificity determining positions (SDP) using a set of human immunodeficiency virus protease-inhibitor genotype-phenotype data and corresponding resistance mutation scores from the Stanford University HIV Drug Resistance Database, and a data set of protein families with experimentally annotated SDPs. For both data sets, SigniSite was found to outperform SPEER. SigniSite is available at: http://www.cbs.dtu.dk/services/SigniSite/. PMID:23761454

  19. PROMALS web server for accurate multiple protein sequence alignments.

    PubMed

    Pei, Jimin; Kim, Bong-Hyun; Tang, Ming; Grishin, Nick V

    2007-07-01

    Multiple sequence alignments are essential in homology inference, structure modeling, functional prediction and phylogenetic analysis. We developed a web server that constructs multiple protein sequence alignments using PROMALS, a progressive method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS shows higher alignment accuracy than other advanced methods, such as MUMMALS, ProbCons, MAFFT and SPEM. The PROMALS web server takes FASTA format protein sequences as input. The output includes a colored alignment augmented with information about sequence grouping, predicted secondary structures and positional conservation. The PROMALS web server is available at: http://prodata.swmed.edu/promals/ PMID:17452345

  20. Imaging Analysis of Collagen Fiber Networks in Cusps of Porcine Aortic Valves: Effect of their Local Distribution and Alignment on Valve Functionality

    PubMed Central

    Mega, Mor; Marom, Gil; Halevi, Rotem; Hamdan, Ashraf; Bluestein, Danny; Haj-Ali, Rami

    2015-01-01

    The cusps of native Aortic Valve (AV) are composed of collagen bundles embedded in soft tissue, creating a heterogenic tissue with asymmetric alignment in each cusp. This study compares native collagen fiber networks (CFNs) with a goal to better understand their influence on stress distribution and valve kinematics. Images of CFNs from five porcine tricuspid AVs are analyzed and fluid-structure interaction models are generated based on them. Although the valves had similar overall kinematics, the CFNs had distinctive influence on local mechanics. The regions with dilute CFN are more prone to damage since they are subjected to higher stress magnitudes. PMID:26406926

  1. Imaging analysis of collagen fiber networks in cusps of porcine aortic valves: effect of their local distribution and alignment on valve functionality.

    PubMed

    Mega, Mor; Marom, Gil; Halevi, Rotem; Hamdan, Ashraf; Bluestein, Danny; Haj-Ali, Rami

    2016-07-01

    The cusps of native aortic valve (AV) are composed of collagen bundles embedded in soft tissue, creating a heterogenic tissue with asymmetric alignment in each cusp. This study compares native collagen fiber networks (CFNs) with a goal to better understand their influence on stress distribution and valve kinematics. Images of CFNs from five porcine tricuspid AVs are analyzed and fluid-structure interaction models are generated based on them. Although the valves had similar overall kinematics, the CFNs had distinctive influence on local mechanics. The regions with dilute CFN are more prone to damage since they are subjected to higher stress magnitudes. PMID:26406926

  2. DNAAlignEditor: DNA alignment editor tool

    PubMed Central

    Sanchez-Villeda, Hector; Schroeder, Steven; Flint-Garcia, Sherry; Guill, Katherine E; Yamasaki, Masanori; McMullen, Michael D

    2008-01-01

    Background With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among individuals within a species. For very polymorphic species such as maize, this has lead to a need for intuitive, user-friendly software that aids the biologist, often with naïve programming capability, in tracking, editing, displaying, and exporting multiple individual sequence alignments. To fill this need we have developed a novel DNA alignment editor. Results We have generated a nucleotide sequence alignment editor (DNAAlignEditor) that provides an intuitive, user-friendly interface for manual editing of multiple sequence alignments with functions for input, editing, and output of sequence alignments. The color-coding of nucleotide identity and the display of associated quality score aids in the manual alignment editing process. DNAAlignEditor works as a client/server tool having two main components: a relational database that collects the processed alignments and a user interface connected to database through universal data access connectivity drivers. DNAAlignEditor can be used either as a stand-alone application or as a network application with multiple users concurrently connected. Conclusion We anticipate that this software will be of general interest to biologists and population genetics in editing DNA sequence alignments and analyzing natural sequence variation regardless of species, and will be particularly useful for manual alignment editing of sequences in species with high levels of polymorphism. PMID:18366684

  3. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and 3-dimensional structural information

    PubMed Central

    Pei, Jimin; Grishin, Nick V.

    2015-01-01

    SUMMARY Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of 3-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D web server and package are available at http://prodata.swmed.edu/PROMALS3D. PMID:24170408

  4. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

    PubMed

    Pei, Jimin; Grishin, Nick V

    2014-01-01

    Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D. PMID:24170408

  5. Making Health System Performance Measurement Useful to Policy Makers: Aligning Strategies, Measurement and Local Health System Accountability in Ontario

    PubMed Central

    Veillard, Jeremy; Huynh, Tai; Ardal, Sten; Kadandale, Sowmya; Klazinga, Niek S.; Brown, Adalsteinn D.

    2010-01-01

    This study examined the experience of the Ontario Ministry of Health and Long-Term Care in enhancing its stewardship and performance management role by developing a health system strategy map and a strategy-based scorecard through a process of policy reviews and expert consultations, and linking them to accountability agreements. An evaluation of the implementation and of the effects of the policy intervention has been carried out through direct policy observation over three years, document analysis, interviews with decision-makers and systematic discussion of findings with other authors and external reviewers. Cascading strategies at health and local health system levels were identified, and a core set of health system and local health system performance indicators was selected and incorporated into accountability agreements with the Local Health Integration Networks. despite the persistence of such challenges as measurement limitations and lack of systematic linkage to decision-making processes, these activities helped to strengthen substantially the ministry's performance management function. PMID:21286268

  6. Multiple Whole Genome Alignments Without a Reference Organism

    SciTech Connect

    Dubchak, Inna; Poliakov, Alexander; Kislyuk, Andrey; Brudno, Michael

    2009-01-16

    Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric alignment algorithm. The resulting alignments not only represent all of the genomes equally well, but also include all relevant duplications that occurred since the divergence from the last common ancestor. Our algorithm, implemented as a part of the VISTA Genome Pipeline (VGP), was used to align seven vertebrate and sixDrosophila genomes. The resulting whole-genome alignments demonstrate a higher sensitivity and specificity than the pairwise alignments previously available through the VGP and have higher exon alignment accuracy than comparable public whole-genome alignments. Of the multiple alignment methods tested, ours performed the best at aligning genes from multigene families?perhaps the most challenging test for whole-genome alignments. Our whole-genome multiple alignments are available through the VISTA Browser at http://genome.lbl.gov/vista/index.shtml.

  7. On comparing two structured RNA multiple alignments.

    PubMed

    Patel, Vandanaben; Wang, Jason T L; Setia, Shefali; Verma, Anurag; Warden, Charles D; Zhang, Kaizhong

    2010-12-01

    We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple alignments in the blocks. Unlike many other tools that can perform pairwise alignment of either single sequences or structures only, BlockMatch takes into account the characteristics of all the sequences in the blocks along with their consensus structures during the alignment process, thus being able to achieve a high-quality alignment result. We apply BlockMatch to phylogeny reconstruction on a set of 5S rRNA sequences taken from fifteen bacteria species. Experimental results showed that the phylogenetic tree generated by our method is more accurate than the tree constructed based on the widely used ClustalW tool. The BlockMatch algorithm is implemented into a web server, accessible at http://bioinformatics.njit.edu/blockmatch. A jar file of the program is also available for download from the web server. PMID:21121021

  8. Applying Agrep to r-NSA to solve multiple sequences approximate matching.

    PubMed

    Ni, Bing; Wong, Man-Hon; Lam, Chi-Fai David; Leung, Kwong-Sak

    2014-01-01

    This paper addresses the approximate matching problem in a database consisting of multiple DNA sequences, where the proposed approach applies Agrep to a new truncated suffix array, r-NSA. The construction time of the structure is linear to the database size, and the computations of indexing a substring in the structure are constant. The number of characters processed in applying Agrep is analysed theoretically, and the theoretical upper-bound can approximate closely the empirical number of characters, which is obtained through enumerating the characters in the actual structure built. Experiments are carried out using (synthetic) random DNA sequences, as well as (real) genome sequences including Hepatitis-B Virus and X-chromosome. Experimental results show that, compared to the straight-forward approach that applies Agrep to multiple sequences individually, the proposed approach solves the matching problem in much shorter time. The speed-up of our approach depends on the sequence patterns, and for highly similar homologous genome sequences, which are the common cases in real-life genomes, it can be up to several orders of magnitude. PMID:25757245

  9. Alignment validation

    SciTech Connect

    ALICE; ATLAS; CMS; LHCb; Golling, Tobias

    2008-09-06

    The four experiments, ALICE, ATLAS, CMS and LHCb are currently under constructionat CERN. They will study the products of proton-proton collisions at the Large Hadron Collider. All experiments are equipped with sophisticated tracking systems, unprecedented in size and complexity. Full exploitation of both the inner detector andthe muon system requires an accurate alignment of all detector elements. Alignmentinformation is deduced from dedicated hardware alignment systems and the reconstruction of charged particles. However, the system is degenerate which means the data is insufficient to constrain all alignment degrees of freedom, so the techniques are prone to converging on wrong geometries. This deficiency necessitates validation and monitoring of the alignment. An exhaustive discussion of means to validate is subject to this document, including examples and plans from all four LHC experiments, as well as other high energy experiments.

  10. Two-way regulation between cells and aligned collagen fibrils: local 3D matrix formation and accelerated neural differentiation of human decidua parietalis placental stem cells.

    PubMed

    Li, Wen; Zhu, Bofan; Strakova, Zuzana; Wang, Rong

    2014-08-01

    It has been well established that an aligned matrix provides structural and signaling cues to guide cell polarization and cell fate decision. However, the modulation role of cells in matrix remodeling and the feedforward effect on stem cell differentiation have not been studied extensively. In this study, we report on the concerted changes of human decidua parietalis placental stem cells (hdpPSCs) and the highly ordered collagen fibril matrix in response to cell-matrix interaction. With high-resolution imaging, we found the hdpPSCs interacted with the matrix by deforming the cell shape, harvesting the nearby collagen fibrils, and reorganizing the fibrils around the cell body to transform a 2D matrix to a localized 3D matrix. Such a unique 3D matrix prompted high expression of β-1 integrin around the cell body that mediates and facilitates the stem cell differentiation toward neural cells. The study offers insights into the coordinated, dynamic changes at the cell-matrix interface and elucidates cell modulation of its matrix to establish structural and biochemical cues for effective cell growth and differentiation. PMID:25003322

  11. Alignment fixture

    DOEpatents

    Bell, Grover C.; Gibson, O. Theodore

    1980-01-01

    A part alignment fixture is provided which may be used for precise variable lateral and tilt alignment relative to the fixture base of various shaped parts. The fixture may be used as a part holder for machining or inspection of parts or alignment of parts during assembly and the like. The fixture includes a precisely machined diameter disc-shaped hub adapted to receive the part to be aligned. The hub is nested in a guide plate which is adapted to carry two oppositely disposed pairs of positioning wedges so that the wedges may be reciprocatively positioned by means of respective micrometer screws. The sloping faces of the wedges contact the hub at respective quadrants of the hub periphery. The lateral position of the hub relative to the guide plate is adjusted by positioning the wedges with the associated micrometer screws. The tilt of the part is adjusted relative to a base plate, to which the guide plate is pivotally connected by means of a holding plate. Two pairs of oppositely disposed wedges are mounted for reciprocative lateral positioning by means of separate micrometer screws between flanges of the guide plate and the base plate. Once the wedges are positioned to achieve the proper tilt of the part or hub on which the part is mounted relative to the base plate, the fixture may be bolted to a machining, inspection, or assembly device.

  12. ALIGNING JIG

    DOEpatents

    Culver, J.S.; Tunnell, W.C.

    1958-08-01

    A jig or device is described for setting or aligning an opening in one member relative to another member or structure, with a predetermined offset, or it may be used for measuring the amount of offset with which the parts have previously been sct. This jig comprises two blocks rabbeted to each other, with means for securing thc upper block to the lower block. The upper block has fingers for contacting one of the members to be a1igmed, the lower block is designed to ride in grooves within the reference member, and calibration marks are provided to determine the amount of offset. This jig is specially designed to align the collimating slits of a mass spectrometer.

  13. Image alignment

    DOEpatents

    Dowell, Larry Jonathan

    2014-04-22

    Disclosed is a method and device for aligning at least two digital images. An embodiment may use frequency-domain transforms of small tiles created from each image to identify substantially similar, "distinguishing" features within each of the images, and then align the images together based on the location of the distinguishing features. To accomplish this, an embodiment may create equal sized tile sub-images for each image. A "key" for each tile may be created by performing a frequency-domain transform calculation on each tile. A information-distance difference between each possible pair of tiles on each image may be calculated to identify distinguishing features. From analysis of the information-distance differences of the pairs of tiles, a subset of tiles with high discrimination metrics in relation to other tiles may be located for each image. The subset of distinguishing tiles for each image may then be compared to locate tiles with substantially similar keys and/or information-distance metrics to other tiles of other images. Once similar tiles are located for each image, the images may be aligned in relation to the identified similar tiles.

  14. Multiple structure alignment with msTALI

    PubMed Central

    2012-01-01

    Background Multiple structure alignments have received increasing attention in recent years as an alternative to multiple sequence alignments. Although multiple structure alignment algorithms can potentially be applied to a number of problems, they have primarily been used for protein core identification. A method that is capable of solving a variety of problems using structure comparison is still absent. Here we introduce a program msTALI for aligning multiple protein structures. Our algorithm uses several informative features to guide its alignments: torsion angles, backbone Cα atom positions, secondary structure, residue type, surface accessibility, and properties of nearby atoms. The algorithm allows the user to weight the types of information used to generate the alignment, which expands its utility to a wide variety of problems. Results msTALI exhibits competitive results on 824 families from the Homstrad and SABmark databases when compared to Matt and Mustang. We also demonstrate success at building a database of protein cores using 341 randomly selected CATH domains and highlight the contribution of msTALI compared to the CATH classifications. Finally, we present an example applying msTALI to the problem of detecting hinges in a protein undergoing rigid-body motion. Conclusions msTALI is an effective algorithm for multiple structure alignment. In addition to its performance on standard comparison databases, it utilizes clear, informative features, allowing further customization for domain-specific applications. The C++ source code for msTALI is available for Linux on the web at http://ifestos.cse.sc.edu/mstali. PMID:22607234

  15. IUS prerelease alignment

    NASA Technical Reports Server (NTRS)

    Evans, F. A.

    1978-01-01

    Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

  16. PROMALS3D web server for accurate multiple protein sequence and structure alignments.

    PubMed

    Pei, Jimin; Tang, Ming; Grishin, Nick V

    2008-07-01

    Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. PMID:18503087

  17. Alignathon: a competitive assessment of whole-genome alignment methods

    PubMed Central

    Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Harris, Robert S.; Fitzgerald, Stephen; Beal, Kathryn; Seledtsov, Igor; Molodtsov, Vladimir; Raney, Brian J.; Clawson, Hiram; Kim, Jaebum; Kemena, Carsten; Chang, Jia-Ming; Erb, Ionas; Poliakov, Alexander; Hou, Minmei; Herrero, Javier; Kent, William James; Solovyev, Victor; Darling, Aaron E.; Ma, Jian; Notredame, Cedric; Brudno, Michael; Dubchak, Inna; Haussler, David; Paten, Benedict

    2014-01-01

    Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments. PMID:25273068

  18. Alignathon: a competitive assessment of whole-genome alignment methods.

    PubMed

    Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Harris, Robert S; Fitzgerald, Stephen; Beal, Kathryn; Seledtsov, Igor; Molodtsov, Vladimir; Raney, Brian J; Clawson, Hiram; Kim, Jaebum; Kemena, Carsten; Chang, Jia-Ming; Erb, Ionas; Poliakov, Alexander; Hou, Minmei; Herrero, Javier; Kent, William James; Solovyev, Victor; Darling, Aaron E; Ma, Jian; Notredame, Cedric; Brudno, Michael; Dubchak, Inna; Haussler, David; Paten, Benedict

    2014-12-01

    Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments. PMID:25273068

  19. Physician-Hospital Alignment in Orthopedic Surgery.

    PubMed

    Bushnell, Brandon D

    2015-09-01

    The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery. PMID:26375539

  20. Efficient mapping of genomic sequences to optimize multiple pairwise alignment in hybrid cluster platforms.

    PubMed

    Montañola, Alberto; Roig, Concepció; Hernández, Porfidio

    2014-01-01

    Multiple sequence alignment (MSA), used in biocomputing to study similarities between different genomic sequences, is known to require important memory and computation resources. Nowadays, researchers are aligning thousands of these sequences, creating new challenges in order to solve the problem using the available resources efficiently. Determining the efficient amount of resources to allocate is important to avoid waste of them, thus reducing the economical costs required in running for example a specific cloud instance. The pairwise alignment is the initial key step of the MSA problem, which will compute all pair alignments needed. We present a method to determine the optimal amount of memory and computation resources to allocate by the pairwise alignment, and we will validate it through a set of experimental results for different possible inputs. These allow us to determine the best parameters to configure the applications in order to use effectively the available resources of a given system. PMID:25339085

  1. A Multiple-Sequence Variant of the Multiple-Baseline Design: A Strategy for Analysis of Sequence Effects and Treatment Comparison.

    ERIC Educational Resources Information Center

    Noell, George H.; Gresham, Frank M.

    2001-01-01

    Describes design logic and potential uses of a variant of the multiple-baseline design. The multiple-baseline multiple-sequence (MBL-MS) consists of multiple-baseline designs that are interlaced with one another and include all possible sequences of treatments. The MBL-MS design appears to be primarily useful for comparison of treatments taking…

  2. Statistical significance of normalized global alignment.

    PubMed

    Peris, Guillermo; Marzal, Andrés

    2014-03-01

    The comparison of homologous proteins from different species is a first step toward a function assignment and a reconstruction of the species evolution. Though local alignment is mostly used for this purpose, global alignment is important for constructing multiple alignments or phylogenetic trees. However, statistical significance of global alignments is not completely clear, lacking a specific statistical model to describe alignments or depending on computationally expensive methods like Z-score. Recently we presented a normalized global alignment, defined as the best compromise between global alignment cost and length, and showed that this new technique led to better classification results than Z-score at a much lower computational cost. However, it is necessary to analyze the statistical significance of the normalized global alignment in order to be considered a completely functional algorithm for protein alignment. Experiments with unrelated proteins extracted from the SCOP ASTRAL database showed that normalized global alignment scores can be fitted to a log-normal distribution. This fact, obtained without any theoretical support, can be used to derive statistical significance of normalized global alignments. Results are summarized in a table with fitted parameters for different scoring schemes. PMID:24400820

  3. Alignment issues of the SLC linac accelerating structure

    SciTech Connect

    Seeman, J.T.; Adolphsen, C.; Decker, F.J.; Fischer, G.; Hodgson, J.; Pennacchi, R.; Perkins, C.; Pietryka, M.

    1991-05-01

    The accelerating structure of the Stanford Linear Collider (SLC) is required to be aligned to 100--200 {mu}m rms. Alignment at such a level will reduce transverse wakefield effects sufficiently so that only a small emittance enlargement of the beam is expected during acceleration to 50 GeV with up to 7 {times} 10{sup 10} particles per bunch. This report describes many aspects of the alignment including global alignment, local alignment, construction of the accelerating cavities, active controls of the structure alignment, external constraints, temperature and airflow effects, and alignment stability. 9 refs., 8 figs.

  4. The interplanetary magnetic field B[sub y] effects on large-scale field-aligned currents near local noon: Contributions from cusp part and noncusp part

    SciTech Connect

    Yamauchi, M.; Lundin, R.; Woch, J. )

    1993-04-01

    latitudinals develop a model to account for the effect of the interplanetary magnetic field (IMF) B[sub y] component on the dayside field-aligned currents (FACs). As part of the model the FACs are divided into a [open quotes]cusp part[close quotes] and a [open quotes]noncusp part[close quotes]. The authors then propose that the cusp part FACs shift in the longitudinal direction while the noncusplike part FACs shift in both longitudinal and latitudinal directions in response to the y component of the IMF. If combined, it is observed that the noncusp part FAC is found poleward of the cusp part FAC system when the y component of the IMF is large. These two FAC systems flow in the same direction. They reinforce one another, creating a strong FAC, termed the DPY-FAC. The model also predicts that the polewardmost part of the DPY-FAC flows on closed field lines, even in regions conventionally occupied by the polar cap. Results of the model are successfully compared with particle and magnetic field data from Viking missions.

  5. De novo genome assembly of the economically important weed horseweed using integrated data from multiple sequencing platforms.

    PubMed

    Peng, Yanhui; Lai, Zhao; Lane, Thomas; Nageswara-Rao, Madhugiri; Okada, Miki; Jasieniuk, Marie; O'Geen, Henriette; Kim, Ryan W; Sammons, R Douglas; Rieseberg, Loren H; Stewart, C Neal

    2014-11-01

    Horseweed (Conyza canadensis), a member of the Compositae (Asteraceae) family, was the first broadleaf weed to evolve resistance to glyphosate. Horseweed, one of the most problematic weeds in the world, is a true diploid (2n = 2x = 18), with the smallest genome of any known agricultural weed (335 Mb). Thus, it is an appropriate candidate to help us understand the genetic and genomic bases of weediness. We undertook a draft de novo genome assembly of horseweed by combining data from multiple sequencing platforms (454 GS-FLX, Illumina HiSeq 2000, and PacBio RS) using various libraries with different insertion sizes (approximately 350 bp, 600 bp, 3 kb, and 10 kb) of a Tennessee-accessed, glyphosate-resistant horseweed biotype. From 116.3 Gb (approximately 350× coverage) of data, the genome was assembled into 13,966 scaffolds with 50% of the assembly = 33,561 bp. The assembly covered 92.3% of the genome, including the complete chloroplast genome (approximately 153 kb) and a nearly complete mitochondrial genome (approximately 450 kb in 120 scaffolds). The nuclear genome is composed of 44,592 protein-coding genes. Genome resequencing of seven additional horseweed biotypes was performed. These sequence data were assembled and used to analyze genome variation. Simple sequence repeat and single-nucleotide polymorphisms were surveyed. Genomic patterns were detected that associated with glyphosate-resistant or -susceptible biotypes. The draft genome will be useful to better understand weediness and the evolution of herbicide resistance and to devise new management strategies. The genome will also be useful as another reference genome in the Compositae. To our knowledge, this article represents the first published draft genome of an agricultural weed. PMID:25209985

  6. BinAligner: a heuristic method to align biological networks.

    PubMed

    Yang, Jialiang; Li, Jun; Grünewald, Stefan; Wan, Xiu-Feng

    2013-01-01

    The advances in high throughput omics technologies have made it possible to characterize molecular interactions within and across various species. Alignments and comparison of molecular networks across species will help detect orthologs and conserved functional modules and provide insights on the evolutionary relationships of the compared species. However, such analyses are not trivial due to the complexity of network and high computational cost. Here we develop a mixture of global and local algorithm, BinAligner, for network alignments. Based on the hypotheses that the similarity between two vertices across networks would be context dependent and that the information from the edges and the structures of subnetworks can be more informative than vertices alone, two scoring schema, 1-neighborhood subnetwork and graphlet, were introduced to derive the scoring matrices between networks, besides the commonly used scoring scheme from vertices. Then the alignment problem is formulated as an assignment problem, which is solved by the combinatorial optimization algorithm, such as the Hungarian method. The proposed algorithm was applied and validated in aligning the protein-protein interaction network of Kaposi's sarcoma associated herpesvirus (KSHV) and that of varicella zoster virus (VZV). Interestingly, we identified several putative functional orthologous proteins with similar functions but very low sequence similarity between the two viruses. For example, KSHV open reading frame 56 (ORF56) and VZV ORF55 are helicase-primase subunits with sequence identity 14.6%, and KSHV ORF75 and VZV ORF44 are tegument proteins with sequence identity 15.3%. These functional pairs can not be identified if one restricts the alignment into orthologous protein pairs. In addition, BinAligner identified a conserved pathway between two viruses, which consists of 7 orthologous protein pairs and these proteins are connected by conserved links. This pathway might be crucial for virus packing and

  7. Grain Alignment in Starless Cores

    NASA Astrophysics Data System (ADS)

    Jones, T. J.; Bagley, M.; Krejny, M.; Andersson, B.-G.; Bastien, P.

    2015-01-01

    We present near-IR polarimetry data of background stars shining through a selection of starless cores taken in the K band, probing visual extinctions up to {{A}V}˜ 48. We find that {{P}K}/{{τ }K} continues to decline with increasing AV with a power law slope of roughly -0.5. Examination of published submillimeter (submm) polarimetry of starless cores suggests that by {{A}V}≳ 20 the slope for P versus τ becomes ˜-1, indicating no grain alignment at greater optical depths. Combining these two data sets, we find good evidence that, in the absence of a central illuminating source, the dust grains in dense molecular cloud cores with no internal radiation source cease to become aligned with the local magnetic field at optical depths greater than {{A}V}˜ 20. A simple model relating the alignment efficiency to the optical depth into the cloud reproduces the observations well.

  8. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

    PubMed Central

    Capella-Gutiérrez, Salvador; Silla-Martínez, José M.; Gabaldón, Toni

    2009-01-01

    Summary: Multiple sequence alignments are central to many areas of bioinformatics. It has been shown that the removal of poorly aligned regions from an alignment increases the quality of subsequent analyses. Such an alignment trimming phase is complicated in large-scale phylogenetic analyses that deal with thousands of alignments. Here, we present trimAl, a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone or in multiple combinations, for selecting the most reliable positions in the alignment. These include the proportion of sequences with a gap, the level of amino acid similarity and, if several alignments for the same set of sequences are provided, the level of consistency across different alignments. Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized. Availability: trimAl has been written in C++, it is portable to all platforms. trimAl is freely available for download (http://trimal.cgenomics.org) and can be used online through the Phylemon web server (http://phylemon2.bioinfo.cipf.es/). Supplementary Material is available at http://trimal.cgenomics.org/publications. Contact: tgabaldon@crg.es PMID:19505945

  9. Nearest Alignment Space Termination

    Energy Science and Technology Software Center (ESTSC)

    2006-07-13

    Near Alignment Space Termination (NAST) is the Greengenes algorithm that matches up submitted sequences with the Greengenes database to look for similarities and align the submitted sequences based on those similarities.

  10. Shiva automatic pinhole alignment

    SciTech Connect

    Suski, G.J.

    1980-09-05

    This paper describes a computer controlled closed loop alignment subsystem for Shiva, which represents the first use of video sensors for large laser alignment at LLNL. The techniques used on this now operational subsystem are serving as the basis for all closed loop alignment on Nova, the 200 terawatt successor to Shiva.

  11. Fast statistical alignment.

    PubMed

    Bradley, Robert K; Roberts, Adam; Smoot, Michael; Juvekar, Sudeep; Do, Jaeyoung; Dewey, Colin; Holmes, Ian; Pachter, Lior

    2009-05-01

    We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment--previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo approaches--yet can align thousands of long sequences. Moreover, FSA utilizes an unsupervised query-specific learning procedure for parameter estimation which leads to improved accuracy on benchmark reference alignments in comparison to existing programs. The centroid alignment approach taken by FSA, in combination with its learning procedure, drastically reduces the amount of false-positive alignment on biological data in comparison to that given by other methods. The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/. PMID:19478997

  12. Girder Alignment Plan

    SciTech Connect

    Wolf, Zackary; Ruland, Robert; LeCocq, Catherine; Lundahl, Eric; Levashov, Yurii; Reese, Ed; Rago, Carl; Poling, Ben; Schafer, Donald; Nuhn, Heinz-Dieter; Wienands, Uli; /SLAC

    2010-11-18

    The girders for the LCLS undulator system contain components which must be aligned with high accuracy relative to each other. The alignment is one of the last steps before the girders go into the tunnel, so the alignment must be done efficiently, on a tight schedule. This note documents the alignment plan which includes efficiency and high accuracy. The motivation for girder alignment involves the following considerations. Using beam based alignment, the girder position will be adjusted until the beam goes through the center of the quadrupole and beam finder wire. For the machine to work properly, the undulator axis must be on this line and the center of the undulator beam pipe must be on this line. The physics reasons for the undulator axis and undulator beam pipe axis to be centered on the beam are different, but the alignment tolerance for both are similar. In addition, the beam position monitor must be centered on the beam to preserve its calibration. Thus, the undulator, undulator beam pipe, quadrupole, beam finder wire, and beam position monitor axes must all be aligned to a common line. All relative alignments are equally important, not just, for example, between quadrupole and undulator. We begin by making the common axis the nominal beam axis in the girder coordinate system. All components will be initially aligned to this axis. A more accurate alignment will then position the components relative to each other, without incorporating the girder itself.

  13. Horizontal carbon nanotube alignment.

    PubMed

    Cole, Matthew T; Cientanni, Vito; Milne, William I

    2016-09-21

    The production of horizontally aligned carbon nanotubes offers a rapid means of realizing a myriad of self-assembled near-atom-scale technologies - from novel photonic crystals to nanoscale transistors. The ability to reproducibly align anisotropic nanostructures has huge technological value. Here we review the present state-of-the-art in horizontal carbon nanotube alignment. For both in and ex situ approaches, we quantitatively assess the reported linear packing densities alongside the degree of alignment possible for each of these core methodologies. PMID:27546174

  14. Orthodontics and Aligners

    MedlinePlus

    ... Repairing Chipped Teeth Teeth Whitening Tooth-Colored Fillings Orthodontics and Aligners Straighten teeth for a healthier smile. Orthodontics When consumers think about orthodontics, braces are the ...

  15. Tidal alignment of galaxies

    NASA Astrophysics Data System (ADS)

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

    2015-08-01

    We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact of smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used "nonlinear alignment model," finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the "GI" term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.

  16. Alignability of Optical Interconnects

    NASA Astrophysics Data System (ADS)

    Beech, Russell Scott

    With the continuing drive towards higher speed, density, and functionality in electronics, electrical interconnects become inadequate. Due to optics' high speed and bandwidth, freedom from capacitive loading effects, and freedom from crosstalk, optical interconnects can meet more stringent interconnect requirements. But, an optical interconnect requires additional components, such as an optical source and detector, lenses, holographic elements, etc. Fabrication and assembly of an optical interconnect requires precise alignment of these components. The successful development and deployment of optical interconnects depend on how easily the interconnect components can be aligned and/or how tolerant the interconnect is to misalignments. In this thesis, a method of quantitatively specifying the relative difficulty of properly aligning an optical interconnect is described. Ways of using this theory of alignment to obtain design and packaging guidelines for optical interconnects are examined. The measure of the ease with which an optical interconnect can be aligned, called the alignability, uses the efficiency of power transfer as a measure of alignment quality. The alignability is related to interconnect package design through the overall cost measure, which depends upon various physical parameters of the interconnect, such as the cost of the components and the time required for fabrication and alignment. Through a mutual dependence on detector size, the relationship between an interconnect's alignability and its bandwidth, signal-to-noise ratio, and bit-error -rate is examined. The results indicate that a range of device sizes exists for which given performance threshold values are satisfied. Next, the alignability of integrated planar-optic backplanes is analyzed in detail. The resulting data show that the alignability can be optimized by varying the substrate thickness or the angle of reflection. By including the effects of crosstalk, in a multi-channel backplane, the

  17. Rapid alignment of velocity and magnetic field in magnetohydrodynamic turbulence.

    PubMed

    Matthaeus, W H; Pouquet, A; Mininni, P D; Dmitruk, P; Breech, B

    2008-02-29

    We show that local directional alignment of the velocity and magnetic field fluctuations occurs rapidly in magnetohydrodynamics for a variety of parameters and is seen both in direct numerical simulations and in solar wind data. The phenomenon is due to an alignment between magnetic field and gradients of either pressure or kinetic energy, and is similar to alignment of velocity and vorticity in Navier-Stokes turbulence. This rapid and robust relaxation process leads to a local weakening of nonlinear terms. PMID:18352632

  18. Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model

    PubMed Central

    Neuwald, Andrew F; Liu, Jun S

    2004-01-01

    Background Certain protein families are highly conserved across distantly related organisms and belong to large and functionally diverse superfamilies. The patterns of conservation present in these protein sequences presumably are due to selective constraints maintaining important but unknown structural mechanisms with some constraints specific to each family and others shared by a larger subset or by the entire superfamily. To exploit these patterns as a source of functional information, we recently devised a statistically based approach called contrast hierarchical alignment and interaction network (CHAIN) analysis, which infers the strengths of various categories of selective constraints from co-conserved patterns in a multiple alignment. The power of this approach strongly depends on the quality of the multiple alignments, which thus motivated development of theoretical concepts and strategies to improve alignment of conserved motifs within large sets of distantly related sequences. Results Here we describe a hidden Markov model (HMM), an algebraic system, and Markov chain Monte Carlo (MCMC) sampling strategies for alignment of multiple sequence motifs. The MCMC sampling strategies are useful both for alignment optimization and for adjusting position specific background amino acid frequencies for alignment uncertainties. Associated statistical formulations provide an objective measure of alignment quality as well as automatic gap penalty optimization. Improved alignments obtained in this way are compared with PSI-BLAST based alignments within the context of CHAIN analysis of three protein families: Giα subunits, prolyl oligopeptidases, and transitional endoplasmic reticulum (p97) AAA+ ATPases. Conclusion While not entirely replacing PSI-BLAST based alignments, which likewise may be optimized for CHAIN analysis using this approach, these motif-based methods often more accurately align very distantly related sequences and thus can provide a better measure of

  19. SPEAR3 Construction Alignment

    SciTech Connect

    LeCocq, Catherine; Banuelos, Cristobal; Fuss, Brian; Gaudreault, Francis; Gaydosh, Michael; Griffin, Levirt; Imfeld, Hans; McDougal, John; Perry, Michael; Rogers, Michael; /SLAC

    2005-08-17

    An ambitious seven month shutdown of the existing SPEAR2 synchrotron radiation facility was successfully completed in March 2004 when the first synchrotron light was observed in the new SPEAR3 ring, SPEAR3 completely replaced SPEAR2 with new components aligned on a new highly-flat concrete floor. Devices such as magnets and vacuum chambers had to be fiducialized and later aligned on girder rafts that were then placed into the ring over pre-aligned support plates. Key to the success of aligning this new ring was to ensure that the new beam orbit matched the old SPEAR2 orbit so that existing experimental beamlines would not have to be reoriented. In this presentation a pictorial summary of the Alignment Engineering Group's surveying tasks for the construction of the SPEAR3 ring is provided. Details on the networking and analysis of various surveys throughout the project can be found in the accompanying paper.

  20. Algorithms for Automatic Alignment of Arrays

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Oliker, Leonid; Schreiber, Robert; Sheffler, Thomas J.

    1996-01-01

    Aggregate data objects (such as arrays) are distributed across the processor memories when compiling a data-parallel language for a distributed-memory machine. The mapping determines the amount of communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: an alignment that maps all the objects to an abstract template, followed by a distribution that maps the template to the processors. This paper describes algorithms for solving the various facets of the alignment problem: axis and stride alignment, static and mobile offset alignment, and replication labeling. We show that optimal axis and stride alignment is NP-complete for general program graphs, and give a heuristic method that can explore the space of possible solutions in a number of ways. We show that some of these strategies can give better solutions than a simple greedy approach proposed earlier. We also show how local graph contractions can reduce the size of the problem significantly without changing the best solution. This allows more complex and effective heuristics to be used. We show how to model the static offset alignment problem using linear programming, and we show that loop-dependent mobile offset alignment is sometimes necessary for optimum performance. We describe an algorithm with for determining mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself or can be used to improve performance. We describe an algorithm based on network flow that replicates objects so as to minimize the total amount of broadcast communication in replication.

  1. Protein alignment: Exact versus approximate. An illustration.

    PubMed

    Randić, Milan; Pisanski, Tomaž

    2015-05-30

    We illustrate solving the protein alignment problem exactly using the algorithm VESPA (very efficient search for protein alignment). We have compared our result with the approximate solution obtained with BLAST (basic local alignment search tool) software, which is currently the most widely used for searching for protein alignment. We have selected human and mouse proteins having around 170 amino acids for comparison. The exact solution has found 78 pairs of amino acids, to which one should add 17 individual amino acid alignments giving a total of 95 aligned amino acids. BLAST has identified 64 aligned amino acids which involve pairs of more than two adjacent amino acids. However, the difference between the two outputs is not as large as it may appear, because a number of amino acids that are adjacent have been reported by BLAST as single amino acids. So if one counts all amino acids, whether isolated (single) or in a group of two and more amino acids, then the count for BLAST is 89 and for VESPA is 95, a difference of only six. PMID:25800773

  2. Sparse alignment for robust tensor learning.

    PubMed

    Lai, Zhihui; Wong, Wai Keung; Xu, Yong; Zhao, Cairong; Sun, Mingming

    2014-10-01

    Multilinear/tensor extensions of manifold learning based algorithms have been widely used in computer vision and pattern recognition. This paper first provides a systematic analysis of the multilinear extensions for the most popular methods by using alignment techniques, thereby obtaining a general tensor alignment framework. From this framework, it is easy to show that the manifold learning based tensor learning methods are intrinsically different from the alignment techniques. Based on the alignment framework, a robust tensor learning method called sparse tensor alignment (STA) is then proposed for unsupervised tensor feature extraction. Different from the existing tensor learning methods, L1- and L2-norms are introduced to enhance the robustness in the alignment step of the STA. The advantage of the proposed technique is that the difficulty in selecting the size of the local neighborhood can be avoided in the manifold learning based tensor feature extraction algorithms. Although STA is an unsupervised learning method, the sparsity encodes the discriminative information in the alignment step and provides the robustness of STA. Extensive experiments on the well-known image databases as well as action and hand gesture databases by encoding object images as tensors demonstrate that the proposed STA algorithm gives the most competitive performance when compared with the tensor-based unsupervised learning methods. PMID:25291733

  3. Grain alignment in starless cores

    SciTech Connect

    Jones, T. J.; Bagley, M.; Krejny, M.; Andersson, B.-G.; Bastien, P.

    2015-01-01

    We present near-IR polarimetry data of background stars shining through a selection of starless cores taken in the K band, probing visual extinctions up to A{sub V}∼48. We find that P{sub K}/τ{sub K} continues to decline with increasing A{sub V} with a power law slope of roughly −0.5. Examination of published submillimeter (submm) polarimetry of starless cores suggests that by A{sub V}≳20 the slope for P versus τ becomes ∼−1, indicating no grain alignment at greater optical depths. Combining these two data sets, we find good evidence that, in the absence of a central illuminating source, the dust grains in dense molecular cloud cores with no internal radiation source cease to become aligned with the local magnetic field at optical depths greater than A{sub V}∼20. A simple model relating the alignment efficiency to the optical depth into the cloud reproduces the observations well.

  4. Precision alignment device

    DOEpatents

    Jones, N.E.

    1988-03-10

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam. 5 figs.

  5. Precision alignment device

    DOEpatents

    Jones, Nelson E.

    1990-01-01

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam.

  6. Hybrid vehicle motor alignment

    DOEpatents

    Levin, Michael Benjamin

    2001-07-03

    A rotor of an electric motor for a motor vehicle is aligned to an axis of rotation for a crankshaft of an internal combustion engine having an internal combustion engine and an electric motor. A locator is provided on the crankshaft, a piloting tool is located radially by the first locator to the crankshaft. A stator of the electric motor is aligned to a second locator provided on the piloting tool. The stator is secured to the engine block. The rotor is aligned to the crankshaft and secured thereto.

  7. Aligning parallel arrays to reduce communication

    NASA Technical Reports Server (NTRS)

    Sheffler, Thomas J.; Schreiber, Robert; Gilbert, John R.; Chatterjee, Siddhartha

    1994-01-01

    Axis and stride alignment is an important optimization in compiling data-parallel programs for distributed-memory machines. We previously developed an optimal algorithm for aligning array expressions. Here, we examine alignment for more general program graphs. We show that optimal alignment is NP-complete in this setting, so we study heuristic methods. This paper makes two contributions. First, we show how local graph transformations can reduce the size of the problem significantly without changing the best solution. This allows more complex and effective heuristics to be used. Second, we give a heuristic that can explore the space of possible solutions in a number of ways. We show that some of these strategies can give better solutions than a simple greedy approach proposed earlier. Our algorithms have been implemented; we present experimental results showing their effect on the performance of some example programs running on the CM-5.

  8. Desktop aligner for fabrication of multilayer microfluidic devices

    NASA Astrophysics Data System (ADS)

    Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

    2015-07-01

    Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm-1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices.

  9. Desktop aligner for fabrication of multilayer microfluidic devices

    PubMed Central

    Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

    2015-01-01

    Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm−1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices. PMID:26233409

  10. Refinement by shifting secondary structure elements improves sequence alignments.

    PubMed

    Tong, Jing; Pei, Jimin; Otwinowski, Zbyszek; Grishin, Nick V

    2015-03-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  11. Refinement by shifting secondary structure elements improves sequence alignments

    PubMed Central

    Tong, Jing; Pei, Jimin; Otwinowski, Zbyszek; Grishin, Nick V.

    2015-01-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  12. Antares alignment gimbal positioner

    SciTech Connect

    Day, R.D.; Viswanathan, V.K.; Saxman, A.C.; Lujan, R.E.; Woodfin, G.L.; Sweatt, W.C.

    1981-01-01

    Antares is a 24-beam 40-TW carbon-dioxide (CO/sub 2/) laser fusion system currently under construction at the Los Alamos National Laboratory. The Antares alignment gimbal positioner (AGP) is an optomechanical instrument that will be used for target alignment and alignment of the 24 laser beams, as well as beam quality assessments. The AGP will be capable of providing pointing, focusing, and wavefront optical path difference, as well as aberration information at both helium-neon (He-Ne) and CO/sub 2/ wavelengths. It is designed to allow the laser beams to be aligned to any position within a 1-cm cube to a tolerance of 10 ..mu..m.

  13. EINSTEIN Cluster Alignments Revisited

    NASA Astrophysics Data System (ADS)

    Chambers, S. W.; Melott, A. L.; Miller, C. J.

    2000-12-01

    We have examined whether the major axes of rich galaxy clusters tend to point (in projection) toward their nearest neighboring cluster. We used the data of Ulmer, McMillan and Kowalski, who used x-ray morphology to define position angles. Our cluster samples, with well measured redshifts and updated positions, were taken from the MX Northern Abell Cluster Survey. The usual Kolmogorov-Smirnov test shows no significant alignment signal for nonrandom angles for all separations less than 100 Mpc/h. Refining the null hypothesis, however, with the Wilcoxon rank-sum test, reveals a high confidence signal for alignment. This confidence is highest when we restrict our sample to small nearest neighbor separations. We conclude that we have identified a more powerful tool for testing cluster-cluster alignments. Moreover, there is a strong signal in the data for alignment, consistent with a picture of hierarchical cluster formation in which matter falls into clusters along large scale filamentary structures.

  14. DoSA: Database of Structural Alignments.

    PubMed

    Mahajan, Swapnil; Agarwal, Garima; Iftekhar, Mohammed; Offmann, Bernard; de Brevern, Alexandre G; Srinivasan, Narayanaswamy

    2013-01-01

    Protein structure alignment is a crucial step in protein structure-function analysis. Despite the advances in protein structure alignment algorithms, some of the local conformationally similar regions are mislabeled as structurally variable regions (SVRs). These regions are not well superimposed because of differences in their spatial orientations. The Database of Structural Alignments (DoSA) addresses this gap in identification of local structural similarities obscured in global protein structural alignments by realigning SVRs using an algorithm based on protein blocks. A set of protein blocks is a structural alphabet that abstracts protein structures into 16 unique local structural motifs. DoSA provides unique information about 159,780 conformationally similar and 56,140 conformationally dissimilar SVRs in 74 705 pairwise structural alignments of homologous proteins. The information provided on conformationally similar and dissimilar SVRs can be helpful to model loop regions. It is also conceivable that conformationally similar SVRs with conserved residues could potentially contribute toward functional integrity of homologues, and hence identifying such SVRs could be helpful in understanding the structural basis of protein function. Database URL: http://bo-protscience.fr/dosa/ PMID:23846594

  15. DoSA: Database of Structural Alignments

    PubMed Central

    Mahajan, Swapnil; Agarwal, Garima; Iftekhar, Mohammed; Offmann, Bernard; de Brevern, Alexandre G.; Srinivasan, Narayanaswamy

    2013-01-01

    Protein structure alignment is a crucial step in protein structure–function analysis. Despite the advances in protein structure alignment algorithms, some of the local conformationally similar regions are mislabeled as structurally variable regions (SVRs). These regions are not well superimposed because of differences in their spatial orientations. The Database of Structural Alignments (DoSA) addresses this gap in identification of local structural similarities obscured in global protein structural alignments by realigning SVRs using an algorithm based on protein blocks. A set of protein blocks is a structural alphabet that abstracts protein structures into 16 unique local structural motifs. DoSA provides unique information about 159 780 conformationally similar and 56 140 conformationally dissimilar SVRs in 74 705 pairwise structural alignments of homologous proteins. The information provided on conformationally similar and dissimilar SVRs can be helpful to model loop regions. It is also conceivable that conformationally similar SVRs with conserved residues could potentially contribute toward functional integrity of homologues, and hence identifying such SVRs could be helpful in understanding the structural basis of protein function. Database URL: http://bo-protscience.fr/dosa/ PMID:23846594

  16. Pairwise Sequence Alignment Library

    SciTech Connect

    Jeff Daily, PNNL

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  17. Pairwise Sequence Alignment Library

    Energy Science and Technology Software Center (ESTSC)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprintmore » that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.« less

  18. PDV Probe Alignment Technique

    SciTech Connect

    Whitworth, T L; May, C M; Strand, O T

    2007-10-26

    This alignment technique was developed while performing heterodyne velocimetry measurements at LLNL. There are a few minor items needed, such as a white card with aperture in center, visible alignment laser, IR back reflection meter, and a microscope to view the bridge surface. The work was performed on KCP flyers that were 6 and 8 mils wide. The probes used were Oz Optics manufactured with focal distances of 42mm and 26mm. Both probes provide a spot size of approximately 80?m at 1550nm. The 42mm probes were specified to provide an internal back reflection of -35 to -40dB, and the probe back reflections were measured to be -37dB and -33dB. The 26mm probes were specified as -30dB and both measured -30.5dB. The probe is initially aligned normal to the flyer/bridge surface. This provides a very high return signal, up to -2dB, due to the bridge reflectivity. A white card with a hole in the center as an aperture can be used to check the reflected beam position relative to the probe and launch beam, and the alignment laser spot centered on the bridge, see Figure 1 and Figure 2. The IR back reflection meter is used to measure the dB return from the probe and surface, and a white card or similar object is inserted between the probe and surface to block surface reflection. It may take several iterations between the visible alignment laser and the IR back reflection meter to complete this alignment procedure. Once aligned normal to the surface, the probe should be tilted to position the visible alignment beam as shown in Figure 3, and the flyer should be translated in the X and Y axis to reposition the alignment beam onto the flyer as shown in Figure 4. This tilting of the probe minimizes the amount of light from the bridge reflection into the fiber within the probe while maintaining the alignment as near normal to the flyer surface as possible. When the back reflection is measured after the tilt adjustment, the level should be about -3dB to -6dB higher than the probes

  19. Curriculum Alignment Research Suggests that Alignment Can Improve Student Achievement

    ERIC Educational Resources Information Center

    Squires, David

    2012-01-01

    Curriculum alignment research has developed showing the relationship among three alignment categories: the taught curriculum, the tested curriculum and the written curriculum. Each pair (for example, the taught and the written curriculum) shows a positive impact for aligning those results. Following this, alignment results from the Third…

  20. DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif.

    PubMed

    Greive, Sandra J; Fung, Herman K H; Chechik, Maria; Jenkins, Huw T; Weitzel, Stephen E; Aguiar, Pedro M; Brentnall, Andrew S; Glousieau, Matthieu; Gladyshev, Grigory V; Potts, Jennifer R; Antson, Alfred A

    2016-01-29

    The helix-turn-helix (HTH) motif features frequently in protein DNA-binding assemblies. Viral pac site-targeting small terminase proteins possess an unusual architecture in which the HTH motifs are displayed in a ring, distinct from the classical HTH dimer. Here we investigate how such a circular array of HTH motifs enables specific recognition of the viral genome for initiation of DNA packaging during virus assembly. We found, by surface plasmon resonance and analytical ultracentrifugation, that individual HTH motifs of the Bacillus phage SF6 small terminase bind the packaging regions of SF6 and related SPP1 genome weakly, with little local sequence specificity. Nuclear magnetic resonance chemical shift perturbation studies with an arbitrary single-site substrate suggest that the HTH motif contacts DNA similarly to how certain HTH proteins contact DNA non-specifically. Our observations support a model where specificity is generated through conformational selection of an intrinsically bent DNA segment by a ring of HTHs which bind weakly but cooperatively. Such a system would enable viral gene regulation and control of the viral life cycle, with a minimal genome, conferring a major evolutionary advantage for SPP1-like viruses. PMID:26673721

  1. DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif

    PubMed Central

    Greive, Sandra J.; Fung, Herman K.H.; Chechik, Maria; Jenkins, Huw T.; Weitzel, Stephen E.; Aguiar, Pedro M.; Brentnall, Andrew S.; Glousieau, Matthieu; Gladyshev, Grigory V.; Potts, Jennifer R.; Antson, Alfred A.

    2016-01-01

    The helix-turn-helix (HTH) motif features frequently in protein DNA-binding assemblies. Viral pac site-targeting small terminase proteins possess an unusual architecture in which the HTH motifs are displayed in a ring, distinct from the classical HTH dimer. Here we investigate how such a circular array of HTH motifs enables specific recognition of the viral genome for initiation of DNA packaging during virus assembly. We found, by surface plasmon resonance and analytical ultracentrifugation, that individual HTH motifs of the Bacillus phage SF6 small terminase bind the packaging regions of SF6 and related SPP1 genome weakly, with little local sequence specificity. Nuclear magnetic resonance chemical shift perturbation studies with an arbitrary single-site substrate suggest that the HTH motif contacts DNA similarly to how certain HTH proteins contact DNA non-specifically. Our observations support a model where specificity is generated through conformational selection of an intrinsically bent DNA segment by a ring of HTHs which bind weakly but cooperatively. Such a system would enable viral gene regulation and control of the viral life cycle, with a minimal genome, conferring a major evolutionary advantage for SPP1-like viruses. PMID:26673721

  2. Aligning Standards and Curriculum for Classroom Success.

    ERIC Educational Resources Information Center

    Perna, Daniel M.; Davis, James R.

    This book provides classroom teachers at every grade level and subject the tools and background to effectively work with standards as a guide in their planning. It explains the process by which educators can rearticulate state standards and align the locally rearticulated standards to their curriculum and student performance. Six chapters include:…

  3. Barrel alignment fixture

    NASA Astrophysics Data System (ADS)

    Sheeley, J. D.

    1981-04-01

    Fabrication of slapper type detonator cables requires bonding of a thin barrel over a bridge. Location of the barrel hole with respect to the bridge is critical: the barrel hole must be centered over the bridge uniform spacing on each side. An alignment fixture which permits rapid adjustment of the barrel position with respect to the bridge is described. The barrel is manipulated by pincer-type fingers which are mounted on a small x-y table equipped with micrometer adjustments. Barrel positioning, performed under a binocular microscopy, is rapid and accurate. After alignment, the microscope is moved out of position and an infrared (IR) heat source is aimed at the barrel. A 5-second pulse of infrared heat flows the adhesive under the barrel and bonds it to the cable. Sapphire and Fotoform glass barrels were bonded successfully with the alignment fixture.

  4. Improved docking alignment system

    NASA Technical Reports Server (NTRS)

    Monford, Leo G. (Inventor)

    1988-01-01

    Improved techniques are provided for the alignment of two objects. The present invention is particularly suited for 3-D translation and 3-D rotational alignment of objects in outer space. A camera is affixed to one object, such as a remote manipulator arm of the spacecraft, while the planar reflective surface is affixed to the other object, such as a grapple fixture. A monitor displays in real-time images from the camera such that the monitor displays both the reflected image of the camera and visible marking on the planar reflective surface when the objects are in proper alignment. The monitor may thus be viewed by the operator and the arm manipulated so that the reflective surface is perpendicular to the optical axis of the camera, the roll of the reflective surface is at a selected angle with respect to the camera, and the camera is spaced a pre-selected distance from the reflective surface.

  5. FMIT alignment cart

    SciTech Connect

    Potter, R.C.; Dauelsberg, L.B.; Clark, D.C.; Grieggs, R.J.

    1981-01-01

    The Fusion Materials Irradiation Test (FMIT) Facility alignment cart must perform several functions. It must serve as a fixture to receive the drift-tube girder assembly when it is removed from the linac tank. It must transport the girder assembly from the linac vault to the area where alignment or disassembly is to take place. It must serve as a disassembly fixture to hold the girder while individual drift tubes are removed for repair. It must align the drift tube bores in a straight line parallel to the girder, using an optical system. These functions must be performed without violating any clearances found within the building. The bore tubes of the drift tubes will be irradiated, and shielding will be included in the system for easier maintenance.

  6. Optics Alignment Panel

    NASA Technical Reports Server (NTRS)

    Schroeder, Daniel J.

    1992-01-01

    The Optics Alignment Panel (OAP) was commissioned by the HST Science Working Group to determine the optimum alignment of the OTA optics. The goal was to find the position of the secondary mirror (SM) for which there is no coma or astigmatism in the camera images due to misaligned optics, either tilt or decenter. The despace position was reviewed of the SM and the optimum focus was sought. The results of these efforts are as follows: (1) the best estimate of the aligned position of the SM in the notation of HDOS is (DZ,DY,TZ,TY) = (+248 microns, +8 microns, +53 arcsec, -79 arcsec), and (2) the best focus, defined to be that despace which maximizes the fractional energy at 486 nm in a 0.1 arcsec radius of a stellar image, is 12.2 mm beyond paraxial focus. The data leading to these conclusions, and the estimated uncertainties in the final results, are presented.

  7. MUSE optical alignment procedure

    NASA Astrophysics Data System (ADS)

    Laurent, Florence; Renault, Edgard; Loupias, Magali; Kosmalski, Johan; Anwand, Heiko; Bacon, Roland; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dubois, Jean-Pierre; Dupuy, Christophe; Kelz, Andreas; Lizon, Jean-Louis; Nicklas, Harald; Parès, Laurent; Remillieux, Alban; Seifert, Walter; Valentin, Hervé; Xu, Wenli

    2012-09-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation VLT integral field spectrograph (1x1arcmin² Field of View) developed for the European Southern Observatory (ESO), operating in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently assembling and testing MUSE in the Integration Hall of the Observatoire de Lyon for the Preliminary Acceptance in Europe, scheduled for 2013. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic instrument mechanical structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2011, all MUSE subsystems were integrated, aligned and tested independently in each institute. After validations, the systems were shipped to the P.I. institute at Lyon and were assembled in the Integration Hall This paper describes the end-to-end optical alignment procedure of the MUSE instrument. The design strategy, mixing an optical alignment by manufacturing (plug and play approach) and few adjustments on key components, is presented. We depict the alignment method for identifying the optical axis using several references located in pupil and image planes. All tools required to perform the global alignment between each subsystem are described. The success of this alignment approach is demonstrated by the good results for the MUSE image quality. MUSE commissioning at the VLT (Very Large Telescope) is planned for 2013.

  8. Orientation and Alignment Echoes

    NASA Astrophysics Data System (ADS)

    Karras, G.; Hertz, E.; Billard, F.; Lavorel, B.; Hartmann, J.-M.; Faucher, O.; Gershnabel, Erez; Prior, Yehiam; Averbukh, Ilya Sh.

    2015-04-01

    We present one of the simplest classical systems featuring the echo phenomenon—a collection of randomly oriented free rotors with dispersed rotational velocities. Following excitation by a pair of time-delayed impulsive kicks, the mean orientation or alignment of the ensemble exhibits multiple echoes and fractional echoes. We elucidate the mechanism of the echo formation by the kick-induced filamentation of phase space, and provide the first experimental demonstration of classical alignment echoes in a thermal gas of CO2 molecules excited by a pair of femtosecond laser pulses.

  9. Segment alignment control system

    NASA Technical Reports Server (NTRS)

    Aubrun, JEAN-N.; Lorell, Ken R.

    1988-01-01

    The segmented primary mirror for the LDR will require a special segment alignment control system to precisely control the orientation of each of the segments so that the resulting composite reflector behaves like a monolith. The W.M. Keck Ten Meter Telescope will utilize a primary mirror made up of 36 actively controlled segments. Thus the primary mirror and its segment alignment control system are directly analogous to the LDR. The problems of controlling the segments in the face of disturbances and control/structures interaction, as analyzed for the TMT, are virtually identical to those for the LDR. The two systems are briefly compared.

  10. Laboratory simulation of field-aligned currents

    NASA Technical Reports Server (NTRS)

    Wessel, Frank J.; Rostoker, Norman

    1993-01-01

    A summary of progress during the period Apr. 1992 to Mar. 1993 is provided. Objectives of the research are (1) to simulate, via laboratory experiments, the three terms of the field-aligned current equation; (2) to simulate auroral-arc formation processes by configuring the boundary conditions of the experimental chamber and plasma parameters to produce highly localized return currents at the end of a field-aligned current system; and (3) to extrapolate these results, using theoretical and computational techniques, to the problem of magnetospheric-ionospheric coupling and to compare them with published literature signatures of auroral-arc phenomena.

  11. Curriculum Alignment: Establishing Coherence

    ERIC Educational Resources Information Center

    Gagné, Philippe; Dumont, Laurence; Brunet, Sabine; Boucher, Geneviève

    2013-01-01

    In this paper, we present a step-by-step guide to implement a curricular alignment project, directed at professional development and student support, and developed in a higher education French as a second language department. We outline best practices and preliminary results from our experience and provide ways to adapt our experience to other…

  12. Aligning brains and minds

    PubMed Central

    Tong, Frank

    2012-01-01

    In this issue of Neuron, Haxby and colleagues describe a new method for aligning functional brain activity patterns across participants. Their study demonstrates that objects are similarly represented across different brains, allowing for reliable classification of one person’s brain activity based on another’s. PMID:22017984

  13. Vertical Alignment and Collaboration.

    ERIC Educational Resources Information Center

    Bergman, Donna; Calzada, Lucio; LaPointe, Nancy; Lee, Audra; Sullivan, Lynn

    This study investigated whether vertical (grade level sequence) alignment of the curriculum in conjunction with teacher collaboration would enhance student performance on the Texas Assessment of Academic Skills (TAAS) test in south Texas school districts of various sizes. Surveys were mailed to the office of the superintendent of 47 school…

  14. Optically Aligned Drill Press

    NASA Technical Reports Server (NTRS)

    Adderholdt, Bruce M.

    1994-01-01

    Precise drill press equipped with rotary-indexing microscope. Microscope and drill exchange places when turret rotated. Microscope axis first aligned over future hole, then rotated out of way so drill axis assumes its precise position. New procedure takes less time to locate drilling positions and produces more accurate results. Apparatus adapted to such other machine tools as milling and measuring machines.

  15. Aligned-or Not?

    ERIC Educational Resources Information Center

    Roseman, Jo Ellen; Koppal, Mary

    2015-01-01

    When state leaders and national partners in the development of the Next Generation Science Standards met to consider implementation strategies, states and school districts wanted to know which materials were aligned to the new standards. The answer from the developers was short but not sweet: You won't find much now, and it's going to…

  16. Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties

    PubMed Central

    Neuwald, Andrew F.; Altschul, Stephen F.

    2016-01-01

    We describe a Bayesian Markov chain Monte Carlo (MCMC) sampler for protein multiple sequence alignment (MSA) that, as implemented in the program GISMO and applied to large numbers of diverse sequences, is more accurate than the popular MSA programs MUSCLE, MAFFT, Clustal-Ω and Kalign. Features of GISMO central to its performance are: (i) It employs a “top-down” strategy with a favorable asymptotic time complexity that first identifies regions generally shared by all the input sequences, and then realigns closely related subgroups in tandem. (ii) It infers position-specific gap penalties that favor insertions or deletions (indels) within each sequence at alignment positions in which indels are invoked in other sequences. This favors the placement of insertions between conserved blocks, which can be understood as making up the proteins’ structural core. (iii) It uses a Bayesian statistical measure of alignment quality based on the minimum description length principle and on Dirichlet mixture priors. Consequently, GISMO aligns sequence regions only when statistically justified. This is unlike methods based on the ad hoc, but widely used, sum-of-the-pairs scoring system, which will align random sequences. (iv) It defines a system for exploring alignment space that provides natural avenues for further experimentation through the development of new sampling strategies for more efficiently escaping from suboptimal traps. GISMO’s superior performance is illustrated using 408 protein sets containing, on average, 235 sequences. These sets correspond to NCBI Conserved Domain Database alignments, which have been manually curated in the light of available crystal structures, and thus provide a means to assess alignment accuracy. GISMO fills a different niche than other MSA programs, namely identifying and aligning a conserved domain present within a large, diverse set of full length sequences. The GISMO program is available at http://gismo.igs.umaryland.edu/. PMID

  17. Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.

    PubMed

    Neuwald, Andrew F; Altschul, Stephen F

    2016-05-01

    We describe a Bayesian Markov chain Monte Carlo (MCMC) sampler for protein multiple sequence alignment (MSA) that, as implemented in the program GISMO and applied to large numbers of diverse sequences, is more accurate than the popular MSA programs MUSCLE, MAFFT, Clustal-Ω and Kalign. Features of GISMO central to its performance are: (i) It employs a "top-down" strategy with a favorable asymptotic time complexity that first identifies regions generally shared by all the input sequences, and then realigns closely related subgroups in tandem. (ii) It infers position-specific gap penalties that favor insertions or deletions (indels) within each sequence at alignment positions in which indels are invoked in other sequences. This favors the placement of insertions between conserved blocks, which can be understood as making up the proteins' structural core. (iii) It uses a Bayesian statistical measure of alignment quality based on the minimum description length principle and on Dirichlet mixture priors. Consequently, GISMO aligns sequence regions only when statistically justified. This is unlike methods based on the ad hoc, but widely used, sum-of-the-pairs scoring system, which will align random sequences. (iv) It defines a system for exploring alignment space that provides natural avenues for further experimentation through the development of new sampling strategies for more efficiently escaping from suboptimal traps. GISMO's superior performance is illustrated using 408 protein sets containing, on average, 235 sequences. These sets correspond to NCBI Conserved Domain Database alignments, which have been manually curated in the light of available crystal structures, and thus provide a means to assess alignment accuracy. GISMO fills a different niche than other MSA programs, namely identifying and aligning a conserved domain present within a large, diverse set of full length sequences. The GISMO program is available at http://gismo.igs.umaryland.edu/. PMID:27192614

  18. Phylo-VISTA: An Interactive Visualization Tool for Multiple DNA Sequence Alignments

    SciTech Connect

    Shah, Nameeta; Couronne, Olivier; Pennacchio, Len A.; Brudno, Michael; Batzoglou, Serafim; Bethel, E. Wes; Rubin, Edward M.; Hamann, Bernd; Dubchak, Inna

    2004-04-01

    We have developed Phylo-VISTA (Shah et al., 2003), an interactive software tool for analyzing multiple alignments by visualizing a similarity measure for DNA sequences of multiple species. The complexity of visual presentation is effectively organized using a framework based upon inter-species phylogenetic relationships. The phylogenetic organization supports rapid, user-guided inter-species comparison. To aid in navigation through large sequence datasets, Phylo-VISTA provides a user with the ability to select and view data at varying resolutions. The combination of multi-resolution data visualization and analysis, combined with the phylogenetic framework for inter-species comparison, produces a highly flexible and powerful tool for visual data analysis of multiple sequence alignments.

  19. Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

    PubMed Central

    Bernard, Guillaume; Chan, Cheong Xin; Ragan, Mark A.

    2016-01-01

    Alignment-free (AF) approaches have recently been highlighted as alternatives to methods based on multiple sequence alignment in phylogenetic inference. However, the sensitivity of AF methods to genome-scale evolutionary scenarios is little known. Here, using simulated microbial genome data we systematically assess the sensitivity of nine AF methods to three important evolutionary scenarios: sequence divergence, lateral genetic transfer (LGT) and genome rearrangement. Among these, AF methods are most sensitive to the extent of sequence divergence, less sensitive to low and moderate frequencies of LGT, and most robust against genome rearrangement. We describe the application of AF methods to three well-studied empirical genome datasets, and introduce a new application of the jackknife to assess node support. Our results demonstrate that AF phylogenomics is computationally scalable to multi-genome data and can generate biologically meaningful phylogenies and insights into microbial evolution. PMID:27363362

  20. MUSE alignment onto VLT

    NASA Astrophysics Data System (ADS)

    Laurent, Florence; Renault, Edgard; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dupuy, Christophe; Jarno, Aurélien; Lizon, Jean-Louis; Migniau, Jean-Emmanuel; Nicklas, Harald; Piqueras, Laure

    2014-07-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation Very Large Telescope (VLT) integral field spectrograph developed for the European Southern Observatory (ESO). It combines a 1' x 1' field of view sampled at 0.2 arcsec for its Wide Field Mode (WFM) and a 7.5"x7.5" field of view for its Narrow Field Mode (NFM). Both modes will operate with the improved spatial resolution provided by GALACSI (Ground Atmospheric Layer Adaptive Optics for Spectroscopic Imaging), that will use the VLT deformable secondary mirror and 4 Laser Guide Stars (LGS) foreseen in 2015. MUSE operates in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently commissioning MUSE in the Very Large Telescope for the Preliminary Acceptance in Chile, scheduled for September, 2014. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2012 and 2013, all MUSE subsystems were integrated, aligned and tested to the P.I. institute at Lyon. After successful PAE in September 2013, MUSE instrument was shipped to the Very Large Telescope in Chile where that was aligned and tested in ESO integration hall at Paranal. After, MUSE was directly transported, fully aligned and without any optomechanical dismounting, onto VLT telescope where the first light was overcame the 7th of February, 2014. This paper describes the alignment procedure of the whole MUSE instrument with respect to the Very Large Telescope (VLT). It describes how 6 tons could be move with accuracy better than 0.025mm and less than 0.25 arcmin in order to reach alignment requirements. The success

  1. MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer

    PubMed Central

    Gauthier, Nicholas Paul; Reznik, Ed; Gao, Jianjiong; Sumer, Selcuk Onur; Schultz, Nikolaus; Sander, Chris; Miller, Martin L.

    2016-01-01

    The MutationAligner web resource, available at http://www.mutationaligner.org, enables discovery and exploration of somatic mutation hotspots identified in protein domains in currently (mid-2015) more than 5000 cancer patient samples across 22 different tumor types. Using multiple sequence alignments of protein domains in the human genome, we extend the principle of recurrence analysis by aggregating mutations in homologous positions across sets of paralogous genes. Protein domain analysis enhances the statistical power to detect cancer-relevant mutations and links mutations to the specific biological functions encoded in domains. We illustrate how the MutationAligner database and interactive web tool can be used to explore, visualize and analyze mutation hotspots in protein domains across genes and tumor types. We believe that MutationAligner will be an important resource for the cancer research community by providing detailed clues for the functional importance of particular mutations, as well as for the design of functional genomics experiments and for decision support in precision medicine. MutationAligner is slated to be periodically updated to incorporate additional analyses and new data from cancer genomics projects. PMID:26590264

  2. A max-margin model for efficient simultaneous alignment and folding of RNA sequences

    PubMed Central

    Do, Chuong B.; Foo, Chuan-Sheng; Batzoglou, Serafim

    2008-01-01

    Motivation: The need for accurate and efficient tools for computational RNA structure analysis has become increasingly apparent over the last several years: RNA folding algorithms underlie numerous applications in bioinformatics, ranging from microarray probe selection to de novo non-coding RNA gene prediction. In this work, we present RAF (RNA Alignment and Folding), an efficient algorithm for simultaneous alignment and consensus folding of unaligned RNA sequences. Algorithmically, RAF exploits sparsity in the set of likely pairing and alignment candidates for each nucleotide (as identified by the CONTRAfold or CONTRAlign programs) to achieve an effectively quadratic running time for simultaneous pairwise alignment and folding. RAF's fast sparse dynamic programming, in turn, serves as the inference engine within a discriminative machine learning algorithm for parameter estimation. Results: In cross-validated benchmark tests, RAF achieves accuracies equaling or surpassing the current best approaches for RNA multiple sequence secondary structure prediction. However, RAF requires nearly an order of magnitude less time than other simultaneous folding and alignment methods, thus making it especially appropriate for high-throughput studies. Availability: Source code for RAF is available at:http://contra.stanford.edu/contrafold/ Contact: chuongdo@cs.stanford.edu PMID:18586747

  3. MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer.

    PubMed

    Gauthier, Nicholas Paul; Reznik, Ed; Gao, Jianjiong; Sumer, Selcuk Onur; Schultz, Nikolaus; Sander, Chris; Miller, Martin L

    2016-01-01

    The MutationAligner web resource, available at http://www.mutationaligner.org, enables discovery and exploration of somatic mutation hotspots identified in protein domains in currently (mid-2015) more than 5000 cancer patient samples across 22 different tumor types. Using multiple sequence alignments of protein domains in the human genome, we extend the principle of recurrence analysis by aggregating mutations in homologous positions across sets of paralogous genes. Protein domain analysis enhances the statistical power to detect cancer-relevant mutations and links mutations to the specific biological functions encoded in domains. We illustrate how the MutationAligner database and interactive web tool can be used to explore, visualize and analyze mutation hotspots in protein domains across genes and tumor types. We believe that MutationAligner will be an important resource for the cancer research community by providing detailed clues for the functional importance of particular mutations, as well as for the design of functional genomics experiments and for decision support in precision medicine. MutationAligner is slated to be periodically updated to incorporate additional analyses and new data from cancer genomics projects. PMID:26590264

  4. Inflation by alignment

    SciTech Connect

    Burgess, C.P.; Roest, Diederik

    2015-06-08

    Pseudo-Goldstone bosons (pGBs) can provide technically natural inflatons, as has been comparatively well-explored in the simplest axion examples. Although inflationary success requires trans-Planckian decay constants, f≳M{sub p}, several mechanisms have been proposed to obtain this, relying on (mis-)alignments between potential and kinetic energies in multiple-field models. We extend these mechanisms to a broader class of inflationary models, including in particular the exponential potentials that arise for pGB potentials based on noncompact groups (and so which might apply to moduli in an extra-dimensional setting). The resulting potentials provide natural large-field inflationary models and can predict a larger primordial tensor signal than is true for simpler single-field versions of these models. In so doing we provide a unified treatment of several alignment mechanisms, showing how each emerges as a limit of the more general setup.

  5. Alignments of RNA structures.

    PubMed

    Blin, Guillaume; Denise, Alain; Dulucq, Serge; Herrbach, Claire; Touzet, Hélène

    2010-01-01

    We describe a theoretical unifying framework to express the comparison of RNA structures, which we call alignment hierarchy. This framework relies on the definition of common supersequences for arc-annotated sequences and encompasses the main existing models for RNA structure comparison based on trees and arc-annotated sequences with a variety of edit operations. It also gives rise to edit models that have not been studied yet. We provide a thorough analysis of the alignment hierarchy, including a new polynomial-time algorithm and an NP-completeness proof. The polynomial-time algorithm involves biologically relevant edit operations such as pairing or unpairing nucleotides. It has been implemented in a software, called gardenia, which is available at the Web server http://bioinfo.lifl.fr/RNA/gardenia. PMID:20431150

  6. On the alignment space.

    PubMed

    Shen, Shi-Yi; Wang, Kui; Hu, Gang; Chen, Lu-Sheng; Zhang, Hua; Xia, Shu-Tao

    2005-01-01

    Sequences with generalized errors which are called mutations in bioinformatics and generalized error-correcting codes are studied in this paper. In the areas of bioinformatics, computer science and information theory, sequences with generalized errors are discussed respectively for different aims. Firstly, we give the definitions of alignment distance and Levenshtein distance by expansion sequences and discuss their properties and relations. Then the modular structure theory is introduced for strictly describe the expansion sequences. We show that the expansion modular structures of sequences form a Boolean algebra. As applications of the modular structure theory, we give a new and more strict proof of triangle inequality for alignment distance. At last, the definition and construction of generalized error-correcting codes are studied, and some optimal codes with small length are listed. PMID:17282158

  7. Alignment reference device

    DOEpatents

    Patton, Gail Y.; Torgerson, Darrel D.

    1987-01-01

    An alignment reference device provides a collimated laser beam that minimizes angular deviations therein. A laser beam source outputs the beam into a single mode optical fiber. The output end of the optical fiber acts as a source of radiant energy and is positioned at the focal point of a lens system where the focal point is positioned within the lens. The output beam reflects off a mirror back to the lens that produces a collimated beam.

  8. Nuclear reactor alignment plate configuration

    DOEpatents

    Altman, David A; Forsyth, David R; Smith, Richard E; Singleton, Norman R

    2014-01-28

    An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

  9. Docking alignment system

    NASA Technical Reports Server (NTRS)

    Monford, Leo G. (Inventor)

    1990-01-01

    Improved techniques are provided for alignment of two objects. The present invention is particularly suited for three-dimensional translation and three-dimensional rotational alignment of objects in outer space. A camera 18 is fixedly mounted to one object, such as a remote manipulator arm 10 of the spacecraft, while the planar reflective surface 30 is fixed to the other object, such as a grapple fixture 20. A monitor 50 displays in real-time images from the camera, such that the monitor displays both the reflected image of the camera and visible markings on the planar reflective surface when the objects are in proper alignment. The monitor may thus be viewed by the operator and the arm 10 manipulated so that the reflective surface is perpendicular to the optical axis of the camera, the roll of the reflective surface is at a selected angle with respect to the camera, and the camera is spaced a pre-selected distance from the reflective surface.

  10. Dynamic Alignment at SLS

    SciTech Connect

    Ruland, Robert E.

    2003-04-23

    The relative alignment of components in the storage ring of the Swiss Light Source (SLS) is guaranteed by mechanical means. The magnets are rigidly fixed to 48 girders by means of alignment rails with tolerances of less than {+-}15 {micro}m. The bending magnets, supported by 3 point ball bearings, overlap adjacent girders and thus establish virtual train links between the girders, located near the bending magnet centres. Keeping the distortion of the storage ring geometry within a tolerance of {+-}100 {micro}m in order to guarantee sufficient dynamic apertures, requires continuous monitoring and correction of the girder locations. Two monitoring systems for the horizontal and the vertical direction will be installed to measure displacements of the train link between girders, which are due to ground settings and temperature effects: The hydrostatic levelling system (HLS) gives an absolute vertical reference, while the horizontal positioning system (HPS), which employs low cost linear encoders with sub-micron resolution, measures relative horizontal movements. The girder mover system based on five DC motors per girder allows a dynamic realignment of the storage ring within a working window of more than {+-}1 mm for girder translations and {+-}1 mrad for rotations. We will describe both monitoring systems (HLS and HPS) as well as the applied correction scheme based on the girder movers. We also show simulations indicating that beam based girder alignment takes care of most of the static closed orbit correction.

  11. Alignment and alignment transition of bent core nematics

    NASA Astrophysics Data System (ADS)

    Elamain, Omaima; Hegde, Gurumurthy; Komitov, Lachezar

    2013-07-01

    We report on the alignment of nematics consisting of bimesogen bent core molecules of chlorine substituent of benzene derivative and their binary mixture with rod like nematics. It was found that the alignment layer made from polyimide material, which is usually used for promoting vertical (homeotropic) alignment of rod like nematics, promotes instead a planar alignment of the bent core nematic and its nematic mixtures. At higher concentration of the rod like nematic component in these mixtures, a temperature driven transition from vertical to planar alignment was found near the transition to isotropic phase.

  12. Polar cap arcs: Sun-aligned or cusp-aligned?

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Paxton, L. J.; Zhang, Qinghe; Xing, Zanyang

    2016-08-01

    Polar cap arcs are often called sun-aligned arcs. Satellite observations reveal that polar cap arcs join together at the cusp and are actually cusp aligned. Strong ionospheric plasma velocity shears, thus field aligned currents, were associated with polar arcs and they were likely caused by Kelvin-Helmholtz waves around the low-latitude magnetopause under a northward IMF Bz. The magnetic field lines around the magnetopause join together in the cusp region so are the field aligned currents and particle precipitation. This explains why polar arcs are cusp aligned.

  13. Alignment as a Teacher Variable

    ERIC Educational Resources Information Center

    Porter, Andrew C.; Smithson, John; Blank, Rolf; Zeidner, Timothy

    2007-01-01

    With the exception of the procedures developed by Porter and colleagues (Porter, 2002), other methods of defining and measuring alignment are essentially limited to alignment between tests and standards. Porter's procedures have been generalized to investigating the alignment between content standards, tests, textbooks, and even classroom…

  14. Solar Alignments - Identification and Analysis

    NASA Astrophysics Data System (ADS)

    Belmonte, Juan Antonio

    The sun was such an important divinity in antiquity, and even today, that solar alignments should be expected within a large variety of places and cultures. These are probably the most conspicuous kind of astronomical alignments a field researcher can deal with. The need for a correct identification is thus evident. The different kind of solar phenomena susceptible of being determined by astronomical alignments will be scrutinized, following by the way in which such alignments can materialize in space. It will be shown that analyzing solar alignments is not always an easy task.

  15. MRFalign: protein homology detection through alignment of Markov random fields.

    PubMed

    Ma, Jianzhu; Wang, Sheng; Wang, Zhiyong; Xu, Jinbo

    2014-03-01

    Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs in a protein family. A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection. This paper presents a new homology detection method MRFalign, consisting of three key components: 1) a Markov Random Fields (MRF) representation of a protein family; 2) a scoring function measuring similarity of two MRFs; and 3) an efficient ADMM (Alternating Direction Method of Multipliers) algorithm aligning two MRFs. Compared to HMM that can only model very short-range residue correlation, MRFs can model long-range residue interaction pattern and thus, encode information for the global 3D structure of a protein family. Consequently, MRF-MRF comparison for remote homology detection shall be much more sensitive than HMM-HMM or PSSM-PSSM comparison. Experiments confirm that MRFalign outperforms several popular HMM or PSSM-based methods in terms of both alignment accuracy and remote homology detection and that MRFalign works particularly well for mainly beta proteins. For example, tested on the benchmark SCOP40 (8353 proteins) for homology detection, PSSM-PSSM and HMM-HMM succeed on 48% and 52% of proteins, respectively, at superfamily level, and on 15% and 27% of proteins, respectively, at fold level. In contrast, MRFalign succeeds on 57.3% and 42.5% of proteins at superfamily and fold level, respectively. This study implies that long-range residue interaction patterns are very helpful for sequence-based homology detection. The software is available for download at http://raptorx.uchicago.edu/download/. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2-5. PMID:24675572

  16. TSGC and JSC Alignment

    NASA Technical Reports Server (NTRS)

    Sanchez, Humberto

    2013-01-01

    NASA and the SGCs are, by design, intended to work closely together and have synergistic Vision, Mission, and Goals. The TSGC affiliates and JSC have been working together, but not always in a concise, coordinated, nor strategic manner. Today we have a couple of simple ideas to present about how TSGC and JSC have started to work together in a more concise, coordinated, and strategic manner, and how JSC and non-TSG Jurisdiction members have started to collaborate: Idea I: TSGC and JSC Technical Alignment Idea II: Concept of Clusters.

  17. De Novo Genome Assembly of the Economically Important Weed Horseweed Using Integrated Data from Multiple Sequencing Platforms1[C][W][OPEN

    PubMed Central

    Peng, Yanhui; Lai, Zhao; Lane, Thomas; Nageswara-Rao, Madhugiri; Okada, Miki; Jasieniuk, Marie; O’Geen, Henriette; Kim, Ryan W.; Sammons, R. Douglas; Rieseberg, Loren H.; Stewart, C. Neal

    2014-01-01

    Horseweed (Conyza canadensis), a member of the Compositae (Asteraceae) family, was the first broadleaf weed to evolve resistance to glyphosate. Horseweed, one of the most problematic weeds in the world, is a true diploid (2n = 2x = 18), with the smallest genome of any known agricultural weed (335 Mb). Thus, it is an appropriate candidate to help us understand the genetic and genomic bases of weediness. We undertook a draft de novo genome assembly of horseweed by combining data from multiple sequencing platforms (454 GS-FLX, Illumina HiSeq 2000, and PacBio RS) using various libraries with different insertion sizes (approximately 350 bp, 600 bp, 3 kb, and 10 kb) of a Tennessee-accessed, glyphosate-resistant horseweed biotype. From 116.3 Gb (approximately 350× coverage) of data, the genome was assembled into 13,966 scaffolds with 50% of the assembly = 33,561 bp. The assembly covered 92.3% of the genome, including the complete chloroplast genome (approximately 153 kb) and a nearly complete mitochondrial genome (approximately 450 kb in 120 scaffolds). The nuclear genome is composed of 44,592 protein-coding genes. Genome resequencing of seven additional horseweed biotypes was performed. These sequence data were assembled and used to analyze genome variation. Simple sequence repeat and single-nucleotide polymorphisms were surveyed. Genomic patterns were detected that associated with glyphosate-resistant or -susceptible biotypes. The draft genome will be useful to better understand weediness and the evolution of herbicide resistance and to devise new management strategies. The genome will also be useful as another reference genome in the Compositae. To our knowledge, this article represents the first published draft genome of an agricultural weed. PMID:25209985

  18. Phylogenetic comparison of local length plasticity of the small subunit of nuclear rDNAs among all Hexapoda orders and the impact of hyper-length-variation on alignment.

    PubMed

    Xie, Qiang; Tian, Xiaoxuan; Qin, Yan; Bu, Wenjun

    2009-02-01

    The SSU nrDNA (18S), is one of the most frequently sequenced molecular markers in phylogenetic studies. However, the length-hyper-variation at multiple positions of this gene can affect the accuracy of alignment greatly and this length variation makes alignment across arthropod orders a serious problem. The analyses of Hexapoda phylogeny is such a case. A more clear recognition of the distribution of the length-variable-regions is needed. In this study, the secondary structure of some length-variable-regions in the SSU nrRNA of Arthropoda was adjusted by the principle of co-variation. It is found that the extent of plasticity of some length-variable-region can extraordinarily be higher than 600 bases in hexapods. And the numbers of hyper length-variable-regions are largest in Strepsiptera and Sternorrhyncha (Hemiptera). Our study shows that some length-variable-regions can serve as synapomorphies for some groups. The phylogenetic comparison also suggested that the expansion of a lateral bulge could be the origin of a helix. PMID:19027081

  19. OBSERVATIONS OF ENHANCED RADIATIVE GRAIN ALIGNMENT NEAR HD 97300

    SciTech Connect

    Andersson, B-G; Potter, S. B. E-mail: sbp@saao.ac.z

    2010-09-10

    We have obtained optical multi-band polarimetry toward sightlines through the Chamaeleon I cloud, particularly in the vicinity of the young B9/A0 star HD 97300. We show, in agreement with earlier studies, that the radiation field impinging on the cloud in the projected vicinity of the star is dominated by the flux from the star, as evidenced by a local enhancement in the grain heating. By comparing the differential grain heating with the differential change in the location of the peak of the polarization curve, we show that the grain alignment is enhanced by the increase in the radiation field. We also find a weak, but measurable, variation in the grain alignment with the relative angle between the radiation field anisotropy and the magnetic field direction. Such an anisotropy in the grain alignment is consistent with a unique prediction of modern radiative alignment torque theory and provides direct support for radiatively driven grain alignment.

  20. An Alignment-Free Approach for Eukaryotic ITS2 Annotation and Phylogenetic Inference

    PubMed Central

    Hidalgo-Yanes, Pedro I.; Pérez-Castillo, Yunierkis; Molina-Ruiz, Reinaldo; Marchal, Kathleen; Vasconcelos, Vítor; Antunes, Agostinho

    2011-01-01

    The ITS2 gene class shows a high sequence divergence among its members that have complicated its annotation and its use for reconstructing phylogenies at a higher taxonomical level (beyond species and genus). Several alignment strategies have been implemented to improve the ITS2 annotation quality and its use for phylogenetic inferences. Although, alignment based methods have been exploited to the top of its complexity to tackle both issues, no alignment-free approaches have been able to successfully address both topics. By contrast, the use of simple alignment-free classifiers, like the topological indices (TIs) containing information about the sequence and structure of ITS2, may reveal to be a useful approach for the gene prediction and for assessing the phylogenetic relationships of the ITS2 class in eukaryotes. Thus, we used the TI2BioP (Topological Indices to BioPolymers) methodology [1], [2], freely available at http://ti2biop.sourceforge.net/ to calculate two different TIs. One class was derived from the ITS2 artificial 2D structures generated from DNA strings and the other from the secondary structure inferred from RNA folding algorithms. Two alignment-free models based on Artificial Neural Networks were developed for the ITS2 class prediction using the two classes of TIs referred above. Both models showed similar performances on the training and the test sets reaching values above 95% in the overall classification. Due to the importance of the ITS2 region for fungi identification, a novel ITS2 genomic sequence was isolated from Petrakia sp. This sequence and the test set were used to comparatively evaluate the conventional classification models based on multiple sequence alignments like Hidden Markov based approaches, revealing the success of our models to identify novel ITS2 members. The isolated sequence was assessed using traditional and alignment-free based techniques applied to phylogenetic inference to complement the taxonomy of the Petrakia sp

  1. Graph-based molecular alignment (GMA).

    PubMed

    Marialke, J; Körner, R; Tietze, S; Apostolakis, Joannis

    2007-01-01

    We describe a combined 2D/3D approach for the superposition of flexible chemical structures, which is based on recent progress in the efficient identification of common subgraphs and a gradient-based torsion space optimization algorithm. The simplicity of the approach is reflected in its generality and computational efficiency: the suggested approach neither requires precalculated statistics on the conformations of the molecules nor does it make simplifying assumptions on the topology of the molecules being compared. Furthermore, graph-based molecular alignment produces alignments that are consistent with the chemistry of the molecules as well as their general structure, as it depends on both the local connectivities between atoms and the overall topology of the molecules. We validate this approach on benchmark sets taken from the literature and show that it leads to good results compared to computationally and algorithmically more involved methods. The results suggest that, for most practical purposes, graph-based molecular alignment is a viable alternative to molecular field alignment with respect to structural superposition and leads to structures of comparable quality in a fraction of the time. PMID:17381175

  2. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

    PubMed Central

    Sela, Itamar; Ashkenazy, Haim; Katoh, Kazutaka; Pupko, Tal

    2015-01-01

    Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters. Much effort has recently been devoted to improving the ability to identify unreliable alignment regions. Detecting such unreliable regions was previously shown to be important for downstream analyses relying on MSAs, such as the detection of positive selection. Here we developed GUIDANCE2, a new integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments, used as building blocks in progressive alignment algorithms. We compared GUIDANCE2 with seven methodologies to detect unreliable MSA regions using extensive simulations and empirical benchmarks. We show that GUIDANCE2 outperforms all previously developed methodologies. Furthermore, GUIDANCE2 also provides a set of alternative MSAs which can be useful for downstream analyses. The novel algorithm is implemented as a web-server, available at: http://guidance.tau.ac.il. PMID:25883146

  3. Nuclear reactor internals alignment configuration

    DOEpatents

    Gilmore, Charles B.; Singleton, Norman R.

    2009-11-10

    An alignment system that employs jacking block assemblies and alignment posts around the periphery of the top plate of a nuclear reactor lower internals core shroud to align an upper core plate with the lower internals and the core shroud with the core barrel. The distal ends of the alignment posts are chamfered and are closely received within notches machined in the upper core plate at spaced locations around the outer circumference of the upper core plate. The jacking block assemblies are used to center the core shroud in the core barrel and the alignment posts assure the proper orientation of the upper core plate. The alignment posts may alternately be formed in the upper core plate and the notches may be formed in top plate.

  4. Fourier transform interferometer alignment method.

    PubMed

    Goldberg, Kenneth A; Naulleau, Patrick; Bokor, Jeffrey

    2002-08-01

    A rapid and convenient method has been developed to facilitate the alignment of the image-plane components of point-diffraction interferometers, including the phase-shifting point-diffraction interferometer. In real time, the Fourier transform of the detected image is used to calculate a pseudoimage of the electric field in the image plane of the test optic where thecritical alignment o f variousoptical components is performed. Reconstruction of the pseudoimage is similar to off-axis, Fourier transform holography. Intermediate steps in the alignment procedure are described. Fine alignment is aided by the introduction and optimization of a global-contrast parameter that is easily calculated from the Fourier transform. Additional applications include the alignment of image-plane apertures in general optical systems, the rapid identification of patterned image-plane alignment marks, and the probing of important image-plane field properties. PMID:12153074

  5. Onorbit IMU alignment error budget

    NASA Technical Reports Server (NTRS)

    Corson, R. W.

    1980-01-01

    The Star Tracker, Crew Optical Alignment Sight (COAS), and Inertial Measurement Unit (IMU) from a complex navigation system with a multitude of error sources were combined. A complete list of the system errors is presented. The errors were combined in a rational way to yield an estimate of the IMU alignment accuracy for STS-1. The expected standard deviation in the IMU alignment error for STS-1 type alignments was determined to be 72 arc seconds per axis for star tracker alignments and 188 arc seconds per axis for COAS alignments. These estimates are based on current knowledge of the star tracker, COAS, IMU, and navigation base error specifications, and were partially verified by preliminary Monte Carlo analysis.

  6. Alignment system for encoders

    NASA Technical Reports Server (NTRS)

    Villani, Daniel D. (Inventor)

    1988-01-01

    An improved encoder alignment system is disclosed which provides an indication of the extent of misalignment and a measure of the rate at which the misalignment may be changing. The invention is adapted for use with a conventional encoder which provides a digital coarse word having at least significant bit and a digital fine word having a least significant bit and a most significant bit. The invention generates the exclusive or of the least significant bit of the coarse digital signal and the least significant bit of the fine digital signal to provide a first signal. The invention then generates the exclusive or of the first signal and the complement of the most significant bit of the fine digital signal to provide an output signal which represents the misalignment of the encoder.

  7. Aligned Defrosting Dunes

    NASA Technical Reports Server (NTRS)

    2004-01-01

    17 August 2004 This July 2004 Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a group of aligned barchan sand dunes in the martian north polar region. At the time, the dunes were covered with seasonal frost, but the frost had begun to sublime away, leaving dark spots and dark outlines around the dunes. The surrounding plains exhibit small, diffuse spots that are also the result of subliming seasonal frost. This northern spring image, acquired on a descending ground track (as MGS was moving north to south on the 'night' side of Mars) is located near 78.8oN, 34.8oW. The image covers an area about 3 km (1.9 mi) across and sunlight illuminates the scene from the upper left.

  8. Lunar Alignments - Identification and Analysis

    NASA Astrophysics Data System (ADS)

    González-García, A. César

    Lunar alignments are difficult to establish given the apparent lack of written accounts clearly pointing toward lunar alignments for individual temples. While some individual cases are reviewed and highlighted, the weight of the proof must fall on statistical sampling. Some definitions for the lunar alignments are provided in order to clarify the targets, and thus, some new tools are provided to try to test the lunar hypothesis in several cases, especially in megalithic astronomy.

  9. Cosmological information in the intrinsic alignments of luminous red galaxies

    NASA Astrophysics Data System (ADS)

    Chisari, Nora Elisa; Dvorkin, Cora

    2013-12-01

    The intrinsic alignments of galaxies are usually regarded as a contaminant to weak gravitational lensing observables. The alignment of Luminous Red Galaxies, detected unambiguously in observations from the Sloan Digital Sky Survey, can be reproduced by the linear tidal alignment model of Catelan, Kamionkowski & Blandford (2001) on large scales. In this work, we explore the cosmological information encoded in the intrinsic alignments of red galaxies. We make forecasts for the ability of current and future spectroscopic surveys to constrain local primordial non-Gaussianity and Baryon Acoustic Oscillations (BAO) in the cross-correlation function of intrinsic alignments and the galaxy density field. For the Baryon Oscillation Spectroscopic Survey, we find that the BAO signal in the intrinsic alignments is marginally significant with a signal-to-noise ratio of 1.8 and 2.2 with the current LOWZ and CMASS samples of galaxies, respectively, and increasing to 2.3 and 2.7 once the survey is completed. For the Dark Energy Spectroscopic Instrument and for a spectroscopic survey following the EUCLID redshift selection function, we find signal-to-noise ratios of 12 and 15, respectively. Local type primordial non-Gaussianity, parametrized by fNL = 10, is only marginally significant in the intrinsic alignments signal with signal-to-noise ratios < 2 for the three surveys considered.

  10. Cosmological information in the intrinsic alignments of luminous red galaxies

    SciTech Connect

    Chisari, Nora Elisa; Dvorkin, Cora E-mail: cdvorkin@ias.edu

    2013-12-01

    The intrinsic alignments of galaxies are usually regarded as a contaminant to weak gravitational lensing observables. The alignment of Luminous Red Galaxies, detected unambiguously in observations from the Sloan Digital Sky Survey, can be reproduced by the linear tidal alignment model of Catelan, Kamionkowski and Blandford (2001) on large scales. In this work, we explore the cosmological information encoded in the intrinsic alignments of red galaxies. We make forecasts for the ability of current and future spectroscopic surveys to constrain local primordial non-Gaussianity and Baryon Acoustic Oscillations (BAO) in the cross-correlation function of intrinsic alignments and the galaxy density field. For the Baryon Oscillation Spectroscopic Survey, we find that the BAO signal in the intrinsic alignments is marginally significant with a signal-to-noise ratio of 1.8 and 2.2 with the current LOWZ and CMASS samples of galaxies, respectively, and increasing to 2.3 and 2.7 once the survey is completed. For the Dark Energy Spectroscopic Instrument and for a spectroscopic survey following the EUCLID redshift selection function, we find signal-to-noise ratios of 12 and 15, respectively. Local type primordial non-Gaussianity, parametrized by f{sub NL} = 10, is only marginally significant in the intrinsic alignments signal with signal-to-noise ratios < 2 for the three surveys considered.

  11. Gold Alignment and Internal Dissipation

    NASA Astrophysics Data System (ADS)

    Lazarian, A.

    1997-07-01

    The measures of mechanical alignment are obtained for both prolate and oblate grains whose temperatures are comparable to the grain kinetic energy divided by k, the Boltzmann constant. For such grains, the alignment of angular momentum, J, with the axis of maximal inertia, a, is only partial, which substantially alters the mechanical alignment as compared with the results obtained by Lazarian and Roberge, Hanany, & Messinger under the assumption of perfect alignment. We also describe Gold alignment when the Barnett dissipation is suppressed and derive an analytical expression that relates the measure of alignment to the parameters of grain nonsphericity and the direction of the gas-grain drift. This solution provides the lower limit for the measure of alignment, while the upper limit is given by the method derived by Lazarian. Using the results of a recent study of incomplete internal relaxation by Lazarian & Roberge, we find measures of alignment for the whole range of ratios of grain rotational energy to kTs, where Ts is the grain temperature. To describe alignment for mildly supersonic drifts, we suggest an analytical approach that provides good correspondence with the results of direct numerical simulations by Roberge, Hanany, & Messinger. We also extend our approach to account for simultaneous action of the Gold and Davis-Greenstein mechanisms.

  12. ANTICALIgN: visualizing, editing and analyzing combined nucleotide and amino acid sequence alignments for combinatorial protein engineering.

    PubMed

    Jarasch, Alexander; Kopp, Melanie; Eggenstein, Evelyn; Richter, Antonia; Gebauer, Michaela; Skerra, Arne

    2016-07-01

    ANTIC ALIGN: is an interactive software developed to simultaneously visualize, analyze and modify alignments of DNA and/or protein sequences that arise during combinatorial protein engineering, design and selection. ANTIC ALIGN: combines powerful functions known from currently available sequence analysis tools with unique features for protein engineering, in particular the possibility to display and manipulate nucleotide sequences and their translated amino acid sequences at the same time. ANTIC ALIGN: offers both template-based multiple sequence alignment (MSA), using the unmutated protein as reference, and conventional global alignment, to compare sequences that share an evolutionary relationship. The application of similarity-based clustering algorithms facilitates the identification of duplicates or of conserved sequence features among a set of selected clones. Imported nucleotide sequences from DNA sequence analysis are automatically translated into the corresponding amino acid sequences and displayed, offering numerous options for selecting reading frames, highlighting of sequence features and graphical layout of the MSA. The MSA complexity can be reduced by hiding the conserved nucleotide and/or amino acid residues, thus putting emphasis on the relevant mutated positions. ANTIC ALIGN: is also able to handle suppressed stop codons or even to incorporate non-natural amino acids into a coding sequence. We demonstrate crucial functions of ANTIC ALIGN: in an example of Anticalins selected from a lipocalin random library against the fibronectin extradomain B (ED-B), an established marker of tumor vasculature. Apart from engineered protein scaffolds, ANTIC ALIGN: provides a powerful tool in the area of antibody engineering and for directed enzyme evolution. PMID:27261456

  13. On the alignment of quasars

    NASA Astrophysics Data System (ADS)

    Zhu, X.-F.

    1986-06-01

    Taking the two Savage-Bolton 5 deg x 5 deg regions of optical quasar patrol as samples, a systematic analysis of the number of aligned quasars was made and compared with the random data generated by Monte Carlo method. The statistical result is that, at least for these two samples, there is no clear evidence for alignment.

  14. On the alignment of quasars

    NASA Astrophysics Data System (ADS)

    Zhu, Xing-fen

    1986-06-01

    Taking the two Savage-Bolton 5° × 5° regions of optical quasar patrol as samples, I made a systematic analysis of the number of aligned quasars and compared with the random data generated by Monte Carlo method. The statistical result is that, at least for these two samples, there is no clear evidence for alignment.

  15. Semiautomated improvement of RNA alignments

    PubMed Central

    Andersen, Ebbe S.; Lind-Thomsen, Allan; Knudsen, Bjarne; Kristensen, Susie E.; Havgaard, Jakob H.; Torarinsson, Elfar; Larsen, Niels; Zwieb, Christian; Sestoft, Peter; Kjems, Jørgen; Gorodkin, Jan

    2007-01-01

    We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its integrated analysis tools prevent the introduction of errors when doing alignment editing. SARSE readily connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster: the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture of the SARSE editor makes it a flexible tool to improve all RNA alignments with relatively little human intervention. Online documentation and software are available at http://sarse.ku.dk. PMID:17804647

  16. CATO: The Clone Alignment Tool.

    PubMed

    Henstock, Peter V; LaPan, Peter

    2016-01-01

    High-throughput cloning efforts produce large numbers of sequences that need to be aligned, edited, compared with reference sequences, and organized as files and selected clones. Different pieces of software are typically required to perform each of these tasks. We have designed a single piece of software, CATO, the Clone Alignment Tool, that allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences. The input and output are designed to be compatible with standard data formats, and thus suitable for integration into a clone processing pipeline. CATO provides both sequence alignment and visualizations to facilitate the analysis of cloning experiments. The alignment algorithm matches each of the relevant candidate sequences against each reference sequence. The visualization portion displays three levels of matching: 1) a top-level summary of the top candidate sequences aligned to each reference sequence, 2) a focused alignment view with the nucleotides of matched sequences displayed against one reference sequence, and 3) a pair-wise alignment of a single reference and candidate sequence pair. Users can select the minimum matching criteria for valid clones, edit or swap reference sequences, and export the results to a summary file as part of the high-throughput cloning workflow. PMID:27459605

  17. Drive alignment pays maintenance dividends

    SciTech Connect

    Fedder, R.

    2008-12-15

    Proper alignment of the motor and gear drive on conveying and processing equipment will result in longer bearing and coupling life, along with lower maintenance costs. Selecting an alignment free drive package instead of a traditional foot mounted drive and motor is a major advancement toward these goals. 4 photos.

  18. Lexical alignment in triadic communication

    PubMed Central

    Foltz, Anouschka; Gaspers, Judith; Thiele, Kristina; Stenneken, Prisca; Cimiano, Philipp

    2015-01-01

    Lexical alignment refers to the adoption of one’s interlocutor’s lexical items. Accounts of the mechanisms underlying such lexical alignment differ (among other aspects) in the role assigned to addressee-centered behavior. In this study, we used a triadic communicative situation to test which factors may modulate the extent to which participants’ lexical alignment reflects addressee-centered behavior. Pairs of naïve participants played a picture matching game and received information about the order in which pictures were to be matched from a voice over headphones. On critical trials, participants did or did not hear a name for the picture to be matched next over headphones. Importantly, when the voice over headphones provided a name, it did not match the name that the interlocutor had previously used to describe the object. Participants overwhelmingly used the word that the voice over headphones provided. This result points to non-addressee-centered behavior and is discussed in terms of disrupting alignment with the interlocutor as well as in terms of establishing alignment with the voice over headphones. In addition, the type of picture (line drawing vs. tangram shape) independently modulated lexical alignment, such that participants showed more lexical alignment to their interlocutor for (more ambiguous) tangram shapes compared to line drawings. Overall, the results point to a rather large role for non-addressee-centered behavior during lexical alignment. PMID:25762955

  19. Well-pump alignment system

    DOEpatents

    Drumheller, Douglas S.

    1998-01-01

    An improved well-pump for geothermal wells, an alignment system for a well-pump, and to a method for aligning a rotor and stator within a well-pump, wherein the well-pump has a whistle assembly formed at a bottom portion thereof, such that variations in the frequency of the whistle, indicating misalignment, may be monitored during pumping.

  20. CATO: The Clone Alignment Tool

    PubMed Central

    Henstock, Peter V.; LaPan, Peter

    2016-01-01

    High-throughput cloning efforts produce large numbers of sequences that need to be aligned, edited, compared with reference sequences, and organized as files and selected clones. Different pieces of software are typically required to perform each of these tasks. We have designed a single piece of software, CATO, the Clone Alignment Tool, that allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences. The input and output are designed to be compatible with standard data formats, and thus suitable for integration into a clone processing pipeline. CATO provides both sequence alignment and visualizations to facilitate the analysis of cloning experiments. The alignment algorithm matches each of the relevant candidate sequences against each reference sequence. The visualization portion displays three levels of matching: 1) a top-level summary of the top candidate sequences aligned to each reference sequence, 2) a focused alignment view with the nucleotides of matched sequences displayed against one reference sequence, and 3) a pair-wise alignment of a single reference and candidate sequence pair. Users can select the minimum matching criteria for valid clones, edit or swap reference sequences, and export the results to a summary file as part of the high-throughput cloning workflow. PMID:27459605

  1. Space Mirror Alignment System

    NASA Technical Reports Server (NTRS)

    Jau, Bruno M.; McKinney, Colin; Smythe, Robert F.; Palmer, Dean L.

    2011-01-01

    An optical alignment mirror mechanism (AMM) has been developed with angular positioning accuracy of +/-0.2 arcsec. This requires the mirror s linear positioning actuators to have positioning resolutions of +/-112 nm to enable the mirror to meet the angular tip/tilt accuracy requirement. Demonstrated capabilities are 0.1 arc-sec angular mirror positioning accuracy, which translates into linear positioning resolutions at the actuator of 50 nm. The mechanism consists of a structure with sets of cross-directional flexures that enable the mirror s tip and tilt motion, a mirror with its kinematic mount, and two linear actuators. An actuator comprises a brushless DC motor, a linear ball screw, and a piezoelectric brake that holds the mirror s position while the unit is unpowered. An interferometric linear position sensor senses the actuator s position. The AMMs were developed for an Astrometric Beam Combiner (ABC) optical bench, which is part of an interferometer development. Custom electronics were also developed to accommodate the presence of multiple AMMs within the ABC and provide a compact, all-in-one solution to power and control the AMMs.

  2. Alignment positioning mechanism

    NASA Technical Reports Server (NTRS)

    Fantasia, Peter M. (Inventor)

    1991-01-01

    An alignment positioning mechanism for correcting and compensating for misalignment of structures to be coupled is disclosed. The mechanism comprises a power screw with a base portion and a threaded shank portion. A mounting fixture is provided for rigidly coupling said base portion to the mounting interface of a supporting structure with the axis of the screw perpendicular thereto. A traveling ball nut threaded on the power screw is formed with an external annular arcuate surface configured in the form of a spherical segment and enclosed by a ball nut housing with a conforming arcuate surface for permitting gimballed motion thereon. The ball nut housing is provided with a mounting surface which is positionable in cooperable engagement with the mounting interface of a primary structure to be coupled to the supporting structure. Cooperative means are provided on the ball nut and ball nut housing, respectively, for positioning the ball nut and ball nut housing in relative gimballed position within a predetermined range of relative angular relationship whereby severe structural stresses due to unequal loadings and undesirable bending moments on the mechanism are avoided.

  3. Alignment-Annotator web server: rendering and annotating sequence alignments

    PubMed Central

    Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

    2014-01-01

    Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

  4. Testing the tidal alignment model of galaxy intrinsic alignment

    SciTech Connect

    Blazek, Jonathan; Seljak, Uroš; McQuinn, Matthew E-mail: mmcquinn@berkeley.edu

    2011-05-01

    Weak gravitational lensing has become a powerful probe of large-scale structure and cosmological parameters. Precision weak lensing measurements require an understanding of the intrinsic alignment of galaxy ellipticities, which can in turn inform models of galaxy formation. It is hypothesized that elliptical galaxies align with the background tidal field and that this alignment mechanism dominates the correlation between ellipticities on cosmological scales (in the absence of lensing). We use recent large-scale structure measurements from the Sloan Digital Sky Survey to test this picture with several statistics: (1) the correlation between ellipticity and galaxy overdensity, w{sub g+}; (2) the intrinsic alignment auto-correlation functions; (3) the correlation functions of curl-free, E, and divergence-free, B, modes, the latter of which is zero in the linear tidal alignment theory; (4) the alignment correlation function, w{sub g}(r{sub p},θ), a recently developed statistic that generalizes the galaxy correlation function to account for the angle between the galaxy separation vector and the principle axis of ellipticity. We show that recent measurements are largely consistent with the tidal alignment model and discuss dependence on galaxy luminosity. In addition, we show that at linear order the tidal alignment model predicts that the angular dependence of w{sub g}(r{sub p},θ) is simply w{sub g+}(r{sub p})cos (2θ) and that this dependence is consistent with recent measurements. We also study how stochastic nonlinear contributions to galaxy ellipticity impact these statistics. We find that a significant fraction of the observed LRG ellipticity can be explained by alignment with the tidal field on scales ∼> 10 \\hMpc. These considerations are relevant to galaxy formation and evolution.

  5. ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites

    PubMed Central

    Lelieveld, Stefan H.; Schütte, Judith; Dijkstra, Maurits J.J.; Bawono, Punto; Kinston, Sarah J.; Göttgens, Berthold; Heringa, Jaap; Bonzanni, Nicola

    2016-01-01

    Eukaryotic gene expression is regulated by transcription factors (TFs) binding to promoter as well as distal enhancers. TFs recognize short, but specific binding sites (TFBSs) that are located within the promoter and enhancer regions. Functionally relevant TFBSs are often highly conserved during evolution leaving a strong phylogenetic signal. While multiple sequence alignment (MSA) is a potent tool to detect the phylogenetic signal, the current MSA implementations are optimized to align the maximum number of identical nucleotides. This approach might result in the omission of conserved motifs that contain interchangeable nucleotides such as the ETS motif (IUPAC code: GGAW). Here, we introduce ConBind, a novel method to enhance alignment of short motifs, even if their mutual sequence similarity is only partial. ConBind improves the identification of conserved TFBSs by improving the alignment accuracy of TFBS families within orthologous DNA sequences. Functional validation of the Gfi1b + 13 enhancer reveals that ConBind identifies additional functionally important ETS binding sites that were missed by all other tested alignment tools. In addition to the analysis of known regulatory regions, our web tool is useful for the analysis of TFBSs on so far unknown DNA regions identified through ChIP-sequencing. PMID:26721389

  6. ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites.

    PubMed

    Lelieveld, Stefan H; Schütte, Judith; Dijkstra, Maurits J J; Bawono, Punto; Kinston, Sarah J; Göttgens, Berthold; Heringa, Jaap; Bonzanni, Nicola

    2016-05-01

    Eukaryotic gene expression is regulated by transcription factors (TFs) binding to promoter as well as distal enhancers. TFs recognize short, but specific binding sites (TFBSs) that are located within the promoter and enhancer regions. Functionally relevant TFBSs are often highly conserved during evolution leaving a strong phylogenetic signal. While multiple sequence alignment (MSA) is a potent tool to detect the phylogenetic signal, the current MSA implementations are optimized to align the maximum number of identical nucleotides. This approach might result in the omission of conserved motifs that contain interchangeable nucleotides such as the ETS motif (IUPAC code: GGAW). Here, we introduce ConBind, a novel method to enhance alignment of short motifs, even if their mutual sequence similarity is only partial. ConBind improves the identification of conserved TFBSs by improving the alignment accuracy of TFBS families within orthologous DNA sequences. Functional validation of the Gfi1b + 13 enhancer reveals that ConBind identifies additional functionally important ETS binding sites that were missed by all other tested alignment tools. In addition to the analysis of known regulatory regions, our web tool is useful for the analysis of TFBSs on so far unknown DNA regions identified through ChIP-sequencing. PMID:26721389

  7. Advanced Mask Aligner Lithography (AMALITH)

    NASA Astrophysics Data System (ADS)

    Voelkel, Reinhard; Vogler, Uwe; Bramati, Arianna

    2015-03-01

    Mask aligner lithography is very attractive for less-critical lithography layers and is widely used for LED, display, CMOS image sensor, micro-fluidics and MEMS manufacturing. Mask aligner lithography is also a preferred choice the semiconductor back-end for 3D-IC, TSV interconnects, advanced packaging (AdP) and wafer-level-packaging (WLP). Mask aligner lithography is a mature technique based on shadow printing and has not much changed since the 1980s. In shadow printing lithography a geometric pattern is transferred by free-space propagation from a photomask to a photosensitive layer on a wafer. The inherent simplicity of the pattern transfer offers ease of operation, low maintenance, moderate capital expenditure, high wafers-per-hour (WPH) throughput, and attractive cost-of-ownership (COO). Advanced mask aligner lithography (AMALITH) comprises different measures to improve shadow printing lithography beyond current limits. The key enabling technology for AMALITH is a novel light integrator systems, referred to as MO Exposure Optics® (MOEO). MOEO allows to fully control and shape the properties of the illumination light in a mask aligner. Full control is the base for accurate simulation and optimization of the shadow printing process (computational lithography). Now photolithography enhancement techniques like customized illumination, optical proximity correction (OPC), phase masks (AAPSM), half-tone lithography and Talbot lithography could be used in mask aligner lithography. We summarize the recent progress in advanced mask aligner lithography (AMALITH) and discuss possible measures to further improve shadow printing lithography.

  8. Recursive dynamic programming for adaptive sequence and structure alignment

    SciTech Connect

    Thiele, R.; Zimmer, R.; Lengauer, T.

    1995-12-31

    We propose a new alignment procedure that is capable of aligning protein sequences and structures in a unified manner. Recursive dynamic programming (RDP) is a hierarchical method which, on each level of the hierarchy, identifies locally optimal solutions and assembles them into partial alignments of sequences and/or structures. In contrast to classical dynamic programming, RDP can also handle alignment problems that use objective functions not obeying the principle of prefix optimality, e.g. scoring schemes derived from energy potentials of mean force. For such alignment problems, RDP aims at computing solutions that are near-optimal with respect to the involved cost function and biologically meaningful at the same time. Towards this goal, RDP maintains a dynamic balance between different factors governing alignment fitness such as evolutionary relationships and structural preferences. As in the RDP method gaps are not scored explicitly, the problematic assignment of gap cost parameters is circumvented. In order to evaluate the RDP approach we analyse whether known and accepted multiple alignments based on structural information can be reproduced with the RDP method.

  9. Aligning for Innovation - Alignment Strategy to Drive Innovation

    NASA Technical Reports Server (NTRS)

    Johnson, Hurel; Teltschik, David; Bussey, Horace, Jr.; Moy, James

    2010-01-01

    With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

  10. Alignment and nonlinear elasticity in biopolymer gels

    NASA Astrophysics Data System (ADS)

    Feng, Jingchen; Levine, Herbert; Mao, Xiaoming; Sander, Leonard M.

    2015-04-01

    We present a Landau-type theory for the nonlinear elasticity of biopolymer gels with a part of the order parameter describing induced nematic order of fibers in the gel. We attribute the nonlinear elastic behavior of these materials to fiber alignment induced by strain. We suggest an application to contact guidance of cell motility in tissue. We compare our theory to simulation of a disordered lattice model for biopolymers. We treat homogeneous deformations such as simple shear, hydrostatic expansion, and simple extension, and obtain good agreement between theory and simulation. We also consider a localized perturbation which is a simple model for a contracting cell in a medium.