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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NRG1 functions downstream of EDS1 to regulate TIR-NLR-mediated plant immunity in Nicotiana benthamiana
Tiancong Qi,Kyungyong Seong,Daniela P. T. Thomazella,Joonyoung Ryan Kim,Julie Pham,Eunyoung Seo,Myeong-Je Cho,Alex Schultink,Brian J. Staskawicz +8 more
TL;DR: This study demonstrates that NRG1 is a key component that acts downstream of EDS1 to mediate various TNL signaling pathways, including Roq1 and RPP1-mediated HR, resistance to Xanthomonas and Pseudomonas, and XopQ-regulated transcriptional changes in N. benthamiana.
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Genome-Based Taxonomic Classification of Bacteroidetes.
Richard L. Hahnke,Jan P. Meier-Kolthoff,Marina García-López,Supratim Mukherjee,Marcel Huntemann,Natalia Ivanova,Tanja Woyke,Nikos C. Kyrpides,Hans-Peter Klenk,Markus Göker +9 more
TL;DR: A large collection of type-strain genomes from Bacteroidetes and closely related phyla are assessed based on the principles of phylogenetic classification and trees inferred from genome-scale data and corrected G+C content values have a significantly better fit to the phylogeny.
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Functional metagenomic analysis reveals rivers are a reservoir for diverse antibiotic resistance genes.
TL;DR: The study suggests that waste water disposal increases the reservoir of resistance mechanisms in the environment either by addition of resistance genes or by input of agents selective for resistant phenotypes.
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IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.
David Paez-Espino,I. Min A. Chen,Krishna Palaniappan,Anna Ratner,Ken Chu,Ernest Szeto,Manoj Pillay,Jinghua Huang,Victor Markowitz,Torben Nielsen,Marcel Huntemann,T. B. K. Reddy,Georgios A. Pavlopoulos,Matthew B. Sullivan,Barbara J. Campbell,Feng Chen,Katherine D. McMahon,Steve J. Hallam,Vincent J. Denef,Ricardo Cavicchioli,Sean M. Caffrey,Wolfgang R. Streit,John Webster,Kim M. Handley,Ghasem Hosseini Salekdeh,Nicolas Tsesmetzis,João C. Setubal,Phillip B. Pope,Wen Tso Liu,Adam R. Rivers,Natalia Ivanova,Nikos C. Kyrpides +31 more
TL;DR: IMG/VR is presented, the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples, serving as an essential resource in the viral genomics community.
Journal ArticleDOI
Fast search of thousands of short-read sequencing experiments
Brad Solomon,Carl Kingsford +1 more
TL;DR: This work introduces Sequence Bloom Trees (SBTs), a method for querying thousands of short-read sequencing experiments by sequence, 162 times faster than existing approaches, which is used to search large data archives for all experiments that involve a given sequence.
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
Initial sequencing and comparative analysis of the mouse genome.
Robert H. Waterston,Kerstin Lindblad-Toh,Ewan Birney,Jane Rogers,Josep F. Abril,Pankaj K. Agarwal,Richa Agarwala,Rachel Ainscough,Marina Alexandersson,Peter An,Stylianos E. Antonarakis,John Attwood,Robert Baertsch,J Bailey,K F Barlow,Stephan Beck,Eric Berry,Bruce W. Birren,Toby Bloom,Peer Bork,Marc Botcherby,Nicolas Bray,Michael R. Brent,Daniel G. Brown,Daniel G. Brown,Stephen D. Brown,Carol J. Bult,John Burton,Jonathan Butler,R. D. Campbell,Piero Carninci,Simon Cawley,Francesca Chiaromonte,Asif T. Chinwalla,Deanna M. Church,Michele Clamp,C M Clee,Francis S. Collins,Lisa Cook,Richard R. Copley,Alan Coulson,Olivier Couronne,James Cuff,Val Curwen,Tim Cutts,Mark J. Daly,Robert David,Joy Davies,Kimberly D. Delehaunty,Justin Deri,Emmanouil T. Dermitzakis,Colin N. Dewey,Nicholas J. Dickens,Mark Diekhans,Sheila Dodge,Inna Dubchak,Diane M. Dunn,Sean R. Eddy,Laura Elnitski,Richard D. Emes,Pallavi Eswara,Eduardo Eyras,Adam Felsenfeld,Ginger A. Fewell,Paul Flicek,Karen Foley,Wayne N. Frankel,Lucinda Fulton,Robert S. Fulton,Terrence S. Furey,Diane Gage,Richard A. Gibbs,Gustavo Glusman,Sante Gnerre,Nick Goldman,Leo Goodstadt,Darren Grafham,Tina Graves,Eric D. Green,Simon G. Gregory,Roderic Guigó,Mark S. Guyer,Ross C. Hardison,David Haussler,Yoshihide Hayashizaki,Deana W. LaHillier,Angela S. Hinrichs,Wratko Hlavina,Timothy Holzer,Fan Hsu,Axin Hua,Tim Hubbard,Adrienne Hunt,Ian J. Jackson,David B. Jaffe,L. Steven Johnson,Matthew Jones,Thomas A. Jones,A Joy,Michael Kamal,Elinor K. Karlsson,Donna Karolchik,Arkadiusz Kasprzyk,Jun Kawai,Evan Keibler,Cristyn Kells,W. James Kent,Andrew Kirby,Diana L. Kolbe,Ian F Korf,Raju Kucherlapati,Edward J. Kulbokas,David Kulp,Tom Landers,J. P. Leger,Steven Leonard,Ivica Letunic,Rosie Levine,Jia Li,Ming Li,Christine Lloyd,Susan Lucas,Bin Ma,Donna Maglott,Elaine R. Mardis,Lucy Matthews,Evan Mauceli,John Mayer,Megan McCarthy,W. Richard McCombie,Stuart McLaren,Kirsten McLay,John Douglas Mcpherson,James Meldrim,Beverley Meredith,Jill P. Mesirov,Webb Miller,Tracie L. Miner,Emmanuel Mongin,Kate Montgomery,Michael J. Morgan,Richard Mott,James C. Mullikin,Donna M. Muzny,William E. Nash,Joanne O. Nelson,Michael N. Nhan,Robert Nicol,Zemin Ning,Chad Nusbaum,Michael J. O’Connor,Yasushi Okazaki,Karen Oliver,Emma Overton-Larty,Lior Pachter,Genís Parra,Kymberlie H. Pepin,Jane Peterson,Pavel A. Pevzner,Robert W. Plumb,Craig Pohl,Alex Poliakov,Tracy C. Ponce,Chris P. Ponting,Simon C. Potter,Michael A. Quail,Alexandre Reymond,Bruce A. Roe,Krishna M. Roskin,Edward M. Rubin,Alistair G. Rust,Ralph Santos,Victor Sapojnikov,Brian Schultz,Jörg Schultz,Matthias S. Schwartz,Scott Schwartz,Carol Scott,Steven Seaman,Steve Searle,Ted Sharpe,Andrew Sheridan,Ratna Shownkeen,Sarah Sims,Jonathan Singer,Guy Slater,Arian F.A. Smit,Douglas Smith,Brian Spencer,Arne Stabenau,Nicole Stange-Thomann,Charles W. Sugnet,Mikita Suyama,Glenn Tesler,Johanna Thompson,David Torrents,Evanne Trevaskis,John Tromp,Catherine Ucla,Abel Ureta-Vidal,Jade P. Vinson,Andrew von Niederhausern,Claire M. Wade,Melanie M. Wall,R. J. Weber,Robert B. Weiss,Michael C. Wendl,Anthony P. West,Kris A. Wetterstrand,Raymond Wheeler,Simon Whelan,Jamey Wierzbowski,David Willey,Sophie Williams,Richard K. Wilson,Eitan E. Winter,Kim C. Worley,Dudley Wyman,Shan Yang,Shiaw Pyng Yang,Evgeny M. Zdobnov,Michael C. Zody,Eric S. Lander +222 more
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.