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
More filters
Journal ArticleDOI
Computational approaches to natural product discovery.
TL;DR: It is argued that the development of algorithms to mine the continuously increasing amounts of (meta)genomic data will enable the promise of genome mining to be realized and provide a vision of what natural product discovery might look like in the future.
Journal ArticleDOI
The house spider genome reveals an ancient whole-genome duplication during arachnid evolution
Evelyn E. Schwager,Evelyn E. Schwager,Prashant P. Sharma,Thomas H. Clarke,Thomas H. Clarke,Thomas H. Clarke,Daniel J. Leite,Torsten Wierschin,Matthias Pechmann,Yasuko Akiyama-Oda,Lauren A. Esposito,Jesper Bechsgaard,Trine Bilde,Alexandra D. Buffry,Hsu Chao,Huyen Dinh,Harshavardhan Doddapaneni,Shannon Dugan,Cornelius Eibner,Cassandra G. Extavour,Peter Funch,Jessica E. Garb,Luis Baudouin Gonzalez,Vanessa L. González,Sam Griffiths-Jones,Yi Han,Cheryl Y. Hayashi,Cheryl Y. Hayashi,Maarten Hilbrant,Maarten Hilbrant,Daniel S.T. Hughes,Ralf Janssen,Sandra L. Lee,Ignacio Maeso,Shwetha C. Murali,Donna M. Muzny,Rodrigo Nunes da Fonseca,Christian L. B. Paese,Jiaxin Qu,Matthew Ronshaugen,Christoph Schomburg,Anna Schoenauer,Angelika Stollewerk,Montserrat Torres-Oliva,Natascha Turetzek,Bram Vanthournout,Bram Vanthournout,John H. Werren,Carsten Wolff,Kim C. Worley,Gregor Bucher,Richard A. Gibbs,Jonathan A. Coddington,Hiroki Oda,Mario Stanke,Nadia A. Ayoub,Nikola-Michael Prpic,Jean-François Flot,Nico Posnien,Stephen Richards,Alistair P. McGregor +60 more
TL;DR: The results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA, and this study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes ofpolyploidization events across eukaryotes.
Journal ArticleDOI
The genome sequence of segmental allotetraploid peanut Arachis hypogaea
David J. Bertioli,Jerry Jenkins,Josh Clevenger,Olga Dudchenko,Dongying Gao,Guillermo Seijo,Soraya C. M. Leal-Bertioli,Longhui Ren,Andrew Farmer,Manish K. Pandey,Sergio Sebastián Samoluk,Brian Abernathy,Gaurav Agarwal,Carolina Ballén-Taborda,Connor Cameron,Jacqueline D. Campbell,Carolina Chavarro,Annapurna Chitikineni,Ye Chu,Sudhansu Dash,Moaine El Baidouri,Moaine El Baidouri,Baozhu Guo,Wei Huang,Kyung Do Kim,Kyung Do Kim,Walid Korani,Sophie Lanciano,Sophie Lanciano,Christopher Lui,Marie Mirouze,Marie Mirouze,Márcio C. Moretzsohn,Melanie Pham,Jin Hee Shin,Jin Hee Shin,Kenta Shirasawa,Senjuti Sinharoy,Avinash Sreedasyam,Nathan T. Weeks,Xinyou Zhang,Zheng Zheng,Ziqi Sun,Lutz Froenicke,Erez Lieberman Aiden,Richard W Michelmore,Rajeev K. Varshney,C. Corley Holbrook,Ethalinda K. S. Cannon,Brian E. Scheffler,Jane Grimwood,Peggy Ozias-Akins,Steven B. Cannon,Scott A. Jackson,Jeremy Schmutz +54 more
TL;DR: The genome sequence of segmental allotetraploid peanut is reported and suggests that diversity generated by genetic deletions and homeologous recombination helped to favor the domestication of Arachis hypogaea over its diploid relatives.
Journal ArticleDOI
Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
Robert D. Stewart,Marc D. Auffret,Amanda Warr,Andrew H. Wiser,Maximilian O. Press,Kyle W. Langford,Ivan Liachko,Timothy J. Snelling,Richard J. Dewhurst,Alan W. Walker,Rainer Roehe,Mick Watson +11 more
TL;DR: This dataset substantially improves the coverage of rumen microbial genomes in the public databases and represents a valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome.
Journal ArticleDOI
MAFFT-DASH: integrated protein sequence and structural alignment.
TL;DR: MAFFT-DASH showed 10–20% improvement over standard MAFFT for MSA problems with weak similarity, in terms of Sum-of-Pairs (SP), a measure of how well a program succeeds at aligning input sequences in comparison to a reference alignment.
References
More filters
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.