BLAST+: architecture and applications.
Christiam Camacho,George Coulouris,Vahram Avagyan,Ning Ma,Jason S. Papadopoulos,Kevin Bealer,Thomas L. Madden +6 more
TLDR
The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences.Abstract:
Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications. We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site. The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications.read more
Citations
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Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants
Pascal Schläpfer,Peifen Zhang,Chuan Wang,Taehyong Kim,Michael Banf,Lee Chae,Kate Dreher,Arvind K. Chavali,Ricardo Nilo-Poyanco,Thomas Bernard,Daniel Kahn,Seung Y. Rhee +11 more
TL;DR: A computational pipeline is presented to identify metabolic enzymes, pathways, and gene clusters from a sequenced genome that implicate local gene duplication and single gene transposition as playing roles in the evolution of plant metabolic gene clusters.
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The Pangenome of Hexaploid Bread Wheat
Juan D. Montenegro,Agnieszka A. Golicz,Agnieszka A. Golicz,Philipp E. Bayer,Bhavna Hurgobin,Bhavna Hurgobin,HueyTyng Lee,HueyTyng Lee,Chon-Kit Kenneth Chan,Paul Visendi,Kaitao Lai,Jaroslav Doležel,Jacqueline Batley,Jacqueline Batley,David Edwards,David Edwards +15 more
TL;DR: An improved reference for Chinese Spring is built and gene diversity across 18 wheat cultivars is explored to provide insight into genome diversity in elite wheat as a basis for genomics-based improvement of this important crop.
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Restoring Cystic Fibrosis Transmembrane Conductance Regulator Function Reduces Airway Bacteria and Inflammation in People with Cystic Fibrosis and Chronic Lung Infections
Katherine B. Hisert,Sonya L. Heltshe,Christopher E. Pope,Peter Jorth,Xia Wu,Rachael M. Edwards,Matthew C. Radey,Frank J. Accurso,Daniel J. Wolter,Gordon Cooke,Ryan J. Adam,S. Carter,B. Grogan,Janice L. Launspach,Seamas C. Donnelly,Charles G. Gallagher,James E. Bruce,David A. Stoltz,Michael J. Welsh,Lucas R. Hoffman,Edward F. McKone,Pradeep K. Singh +21 more
TL;DR: It is found that ivacaftor caused marked reductions in sputum P. aeruginosa density and airway inflammation and produced modest improvements in radiographic lung disease in subjects with G551D‐CFTR mutations, raising the possibility that infection and inflammation may progress independently of CFTR activity once cystic fibrosis lung disease is established.
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Benchmarking fold detection by DaliLite v.5.
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NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira.
Michael Pester,Frank Maixner,David Berry,Thomas Rattei,Hanna Koch,Sebastian Lücker,Boris Nowka,Andreas Richter,Eva Spieck,Elena Lebedeva,Alexander Loy,Michael Wagner,Holger Daims +12 more
TL;DR: This work introduces nxrB, the gene encoding subunit beta of nitrite oxidoreductase, as a functional and phylogenetic marker for Nitrospira, and reveals a previously unrecognized diversity of terrestrial NitroSpira.
References
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Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
BLAT—The BLAST-Like Alignment Tool
TL;DR: How BLAT was optimized is described, which is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.
Journal ArticleDOI
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TL;DR: The results of an international collaboration to produce a high-quality draft sequence of the mouse genome are reported and an initial comparative analysis of the Mouse and human genomes is presented, describing some of the insights that can be gleaned from the two sequences.
Journal ArticleDOI
A greedy algorithm for aligning DNA sequences.
TL;DR: A new greedy alignment algorithm is introduced with particularly good performance and it is shown that it computes the same alignment as does a certain dynamic programming algorithm, while executing over 10 times faster on appropriate data.