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PMID: 9254694 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S. Review

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Nucleic acids research ·Vol. 25 ·No. 17 ·1997-09-01 ·Pages 3389-402

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ

Abstract

The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. 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. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

MeSH Terms
Algorithms Amino Acid Sequence Animals DNA/chemistry Databases, Factual Humans Molecular Sequence Data Proteins/chemistry Sequence Alignment Software
Chemicals
Proteins DNA
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Altschul S F
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. altschul@ncbi.nlm.nih.gov
Madden T L
Schäffer A A
Zhang J
Zhang Z
Miller W
Lipman D J
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/25.17.3389
Email
altschul@ncbi.nlm.nih.gov
Published
1997-09-01
Pages
3389-402
Language
English
Region
England
NLM ID
0411011
PMCID
PMC146917
Subset
IM
Grants
NLM NIH HHS · LM05110 · United States
External Links
PubMed source DOI: 10.1093/nar/25.17.3389 PMC Full Text View journal details
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