Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 1997 Sep 1;25(17):3389-402.
doi: 10.1093/nar/25.17.3389.

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

S F Altschul  1 , T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman
Affiliations
Review

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

S F Altschul et al. Nucleic Acids Res. .

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.

PubMed Disclaimer

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. J Mol Biol. 1989 Jun 20;207(4):647-53 - PubMed
    1. J Mol Biol. 1994 Mar 4;236(4):1067-78 - PubMed
    1. Nat Genet. 1996 Dec;14(4):430-40 - PubMed
    1. Nucleic Acids Res. 1997 Jan 1;25(1):31-6 - PubMed
    1. Virology. 1986 Dec;155(2):418-33 - PubMed

Publication types

-