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. 2013 Jul;41(Web Server issue):W29-33.
doi: 10.1093/nar/gkt282. Epub 2013 Apr 22.

BLAST: a more efficient report with usability improvements

Grzegorz M Boratyn  1 , Christiam Camacho, Peter S Cooper, George Coulouris, Amelia Fong, Ning Ma, Thomas L Madden, Wayne T Matten, Scott D McGinnis, Yuri Merezhuk, Yan Raytselis, Eric W Sayers, Tao Tao, Jian Ye, Irena Zaretskaya
Affiliations

BLAST: a more efficient report with usability improvements

Grzegorz M Boratyn et al. Nucleic Acids Res. 2013 Jul.

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.

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Figures

Figure 1.
Figure 1.
Table of descriptions for a search of the genomic region for the gulonolactone (l-) oxidase gene of Rattus norvegicus (bases 48 898 799–48 921 150 of NC_005114.3) against nt. Selecting the title loads the alignments for that sequence (if needed) and moves the focus to that alignment. Selecting an accession on the right opens a GenBank report on that sequence. The download menu (left side), as well as the GenBank, graphics and distance tree views, can be enabled by selecting checkboxes on the left side. So as not to cover the table, the download menu is shown above where it would actually open. The gear icon on the right side can be used to control the columns shown. Its menu is shown above where it actually opens.
Figure 2.
Figure 2.
Example view of query and selected subject sequences in the graphical sequence viewer. The subject sequences are selected mRNAs found by a megaBLAST search against nt with the genomic region for the gulonolactone (l-) oxidase gene of Rattus norvegicus (bases 48 898 799–48 921 150 of NC_005114.3) as the query. The viewer shows the query sequence at the top of the figure. Next, the Gulo gene feature on the query sequence is shown in green. This track was enabled with the ‘configure’ feature of the viewer. Finally, the subject sequences are shown as ‘cleaned alignments’, which presents an overview of the alignments that groups matches from the same subject sequence with a thin line and adds an accession label. The red color in the subject sequences represents mismatches to the query.
Figure 3.
Figure 3.
Alignments from a search of the genomic region for the gulonolactone (l-) oxidase gene of Rattus norvegicus (bases 48 898 799–48 921 150 of NC_005114.3) against nt. The download menu and links for GenBank and graphic apply only to this subject sequence, but they have the same behavior as described for the descriptions earlier in the text. New navigation aids are part of the alignment display. ‘Next’ (‘previous’) moves the focus of the report to alignments for the next (previous) subject sequences. ‘Descriptions’ takes the focus back to the line for the current subject sequence in the table of descriptions. For subject sequences with more than one match, ‘next match’ and ‘previous match’ move the focus of the report to the next or the previous match for that subject sequence.
Figure 4.
Figure 4.
Automatically generated documentation for the rat genome database. The information is stored in the blastdb_info database and formatted on demand. Information, such as last update, number of sequences and type or sequence (‘genomic’), is automatically generated when the database is constructed. The database curator provides the title and description.
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