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Nucleic Acids Research 2006 34(Web Server issue):W6-W9; doi:10.1093/nar/gkl164
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Published by Oxford University Press 2006
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

BLAST: improvements for better sequence analysis

Jian Ye, Scott McGinnis and Thomas L. Madden*

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA

*To whom correspondence should be addressed. Tel: +1 301 435 5991; Fax: +1 301 480 0814; Email: madden{at}ncbi.nlm.nih.gov

Received February 10, 2006. Revised February 22, 2006. Accepted March 20, 2006.

Basic local alignment search tool (BLAST) is a sequence similarity search program. The National Center for Biotechnology Information (NCBI) maintains a BLAST server with a home page at http://www.ncbi.nlm.nih.gov/BLAST/. We report here on recent enhancements to the results produced by the BLAST server at the NCBI. These include features to highlight mismatches between similar sequences, show where the query was masked for low-complexity sequence, and integrate information about the database sequences from the NCBI Entrez system into the BLAST display. Changes to how the database sequences are fetched have also improved the speed of the report generator.


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