BLAST: a more efficient report with usability improvements

The Basic Local Alignment Search Tool (BLAST) website at the National Center for Biotechnology (NCBI) is an important resource for searching and aligning sequences. A new BLAST report allows faster loading of alignments, adds navigation aids, allows easy downloading of subject sequences and reports...

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Published in	Nucleic acids research Vol. 41; no. W1; pp. W29 - W33
Main Authors	Boratyn, Grzegorz M., Camacho, Christiam, Cooper, Peter S., Coulouris, George, Fong, Amelia, Ma, Ning, Madden, Thomas L., Matten, Wayne T., McGinnis, Scott D., Merezhuk, Yuri, Raytselis, Yan, Sayers, Eric W., Tao, Tao, Ye, Jian, Zaretskaya, Irena
Format	Journal Article
Language	English
Published	England Oxford University Press 01.07.2013
Subjects	Animals Genomics Internet L-Gulonolactone Oxidase - genetics Rats Sequence Alignment - methods Software
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Abstract	The Basic Local Alignment Search Tool (BLAST) website at the National Center for Biotechnology (NCBI) is an important resource for searching and aligning sequences. A new BLAST report allows faster loading of alignments, adds navigation aids, allows easy downloading of subject sequences and reports and has improved usability. Here, we describe these improvements to the BLAST report, discuss design decisions, describe other improvements to the search page and database documentation and outline plans for future development. The NCBI BLAST URL is http://blast.ncbi.nlm.nih.gov.
AbstractList	The Basic Local Alignment Search Tool (BLAST) website at the National Center for Biotechnology (NCBI) is an important resource for searching and aligning sequences. A new BLAST report allows faster loading of alignments, adds navigation aids, allows easy downloading of subject sequences and reports and has improved usability. Here, we describe these improvements to the BLAST report, discuss design decisions, describe other improvements to the search page and database documentation and outline plans for future development. The NCBI BLAST URL is http://blast.ncbi.nlm.nih.gov.The Basic Local Alignment Search Tool (BLAST) website at the National Center for Biotechnology (NCBI) is an important resource for searching and aligning sequences. A new BLAST report allows faster loading of alignments, adds navigation aids, allows easy downloading of subject sequences and reports and has improved usability. Here, we describe these improvements to the BLAST report, discuss design decisions, describe other improvements to the search page and database documentation and outline plans for future development. The NCBI BLAST URL is http://blast.ncbi.nlm.nih.gov. The Basic Local Alignment Search Tool (BLAST) website at the National Center for Biotechnology (NCBI) is an important resource for searching and aligning sequences. A new BLAST report allows faster loading of alignments, adds navigation aids, allows easy downloading of subject sequences and reports and has improved usability. Here, we describe these improvements to the BLAST report, discuss design decisions, describe other improvements to the search page and database documentation and outline plans for future development. The NCBI BLAST URL is http://blast.ncbi.nlm.nih.gov. The Basic Local Alignment Search Tool (BLAST) website at the National Center for Biotechnology (NCBI) is an important resource for searching and aligning sequences. A new BLAST report allows faster loading of alignments, adds navigation aids, allows easy downloading of subject sequences and reports and has improved usability. Here, we describe these improvements to the BLAST report, discuss design decisions, describe other improvements to the search page and database documentation and outline plans for future development. The NCBI BLAST URL is http://blast.ncbi.nlm.nih.gov .
Author	Camacho, Christiam Matten, Wayne T. Merezhuk, Yuri Fong, Amelia Ma, Ning Tao, Tao Madden, Thomas L. Cooper, Peter S. Coulouris, George McGinnis, Scott D. Raytselis, Yan Ye, Jian Boratyn, Grzegorz M. Sayers, Eric W. Zaretskaya, Irena
AuthorAffiliation	National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 45, 8600 Rockville Pike, Bethesda, MD 20894, USA
AuthorAffiliation_xml	– name: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 45, 8600 Rockville Pike, Bethesda, MD 20894, USA
Author_xml	– sequence: 1 givenname: Grzegorz M. surname: Boratyn fullname: Boratyn, Grzegorz M. – sequence: 2 givenname: Christiam surname: Camacho fullname: Camacho, Christiam – sequence: 3 givenname: Peter S. surname: Cooper fullname: Cooper, Peter S. – sequence: 4 givenname: George surname: Coulouris fullname: Coulouris, George – sequence: 5 givenname: Amelia surname: Fong fullname: Fong, Amelia – sequence: 6 givenname: Ning surname: Ma fullname: Ma, Ning – sequence: 7 givenname: Thomas L. surname: Madden fullname: Madden, Thomas L. – sequence: 8 givenname: Wayne T. surname: Matten fullname: Matten, Wayne T. – sequence: 9 givenname: Scott D. surname: McGinnis fullname: McGinnis, Scott D. – sequence: 10 givenname: Yuri surname: Merezhuk fullname: Merezhuk, Yuri – sequence: 11 givenname: Yan surname: Raytselis fullname: Raytselis, Yan – sequence: 12 givenname: Eric W. surname: Sayers fullname: Sayers, Eric W. – sequence: 13 givenname: Tao surname: Tao fullname: Tao, Tao – sequence: 14 givenname: Jian surname: Ye fullname: Ye, Jian – sequence: 15 givenname: Irena surname: Zaretskaya fullname: Zaretskaya, Irena
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/23609542$$D View this record in MEDLINE/PubMed
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References_xml	– volume: 10 start-page: 421 year: 2009 ident: key 20171013135553_gkt282-B2 article-title: BLAST+: architecture and applications publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-10-421 – volume: 34 start-page: W6 year: 2006 ident: key 20171013135553_gkt282-B5 article-title: BLAST: improvements for better sequence analysis publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkl164 – volume: 7 start-page: 649 year: 1997 ident: key 20171013135553_gkt282-B9 article-title: PowerBLAST: a new network BLAST application for interactive or automated sequence analysis and annotation publication-title: Genome Res. doi: 10.1101/gr.7.6.649 – volume: 36 start-page: W5 year: 2008 ident: key 20171013135553_gkt282-B3 article-title: NCBI BLAST: a better web interface publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkn201 – volume: 29 start-page: 2994 year: 2001 ident: key 20171013135553_gkt282-B7 article-title: Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements publication-title: Nucleic Acids Res. doi: 10.1093/nar/29.14.2994 – volume: 32 start-page: W20 year: 2004 ident: key 20171013135553_gkt282-B4 article-title: BLAST: at the core of a powerful and diverse set of sequence analysis tools publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkh435 – volume: 25 start-page: 3389 year: 1997 ident: key 20171013135553_gkt282-B1 article-title: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs publication-title: Nucleic Acids Res. doi: 10.1093/nar/25.17.3389 – volume: 24 start-page: 1757 year: 2008 ident: key 20171013135553_gkt282-B6 article-title: Database indexing for production MegaBLAST searches publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn322 – volume: 7 start-page: 12 year: 2012 ident: key 20171013135553_gkt282-B8 article-title: Domain enhanced lookup time accelerated BLAST publication-title: Biol. Direct. doi: 10.1186/1745-6150-7-12 – reference: 15215342 - Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W20-5 – reference: 22510480 - Biol Direct. 2012;7:12 – reference: 11452024 - Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005 – reference: 9199938 - Genome Res. 1997 Jun;7(6):649-56 – reference: 16845079 - Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W6-9 – reference: 9254694 - Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 – reference: 18567917 - Bioinformatics. 2008 Aug 15;24(16):1757-64 – reference: 18440982 - Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W5-9 – reference: 20003500 - BMC Bioinformatics. 2009;10:421
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