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

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. (1997)

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by Stephen F Altschul , Thomas L Madden , Alejandro A Schäffer , Jinghui Zhang , Zheng Zhang , Webb Miller , David J Lipman

Venue:	Nucleic Acids Res.
Citations:	8556 - 86 self

BibTeX

@ARTICLE{Altschul97gappedblast,
    author = {Stephen F Altschul and Thomas L Madden and Alejandro A Schäffer and Jinghui Zhang and Zheng Zhang and Webb Miller and David J Lipman},
    title = {Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.},
    journal = {Nucleic Acids Res.},
    year = {1997},
    pages = {3389--3402}
}

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Abstract

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.

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