Gapped Blast and PsiBlast: a new generation of protein database search programs

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Gapped Blast and PsiBlast: 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 RESEARCH
Citations:	8572 - 88 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 PsiBlast: a new generation of protein database search programs},
    journal = {NUCLEIC ACIDS RESEARCH},
    year = {1997},
    volume = {25},
    number = {17},
    pages = {3389--3402}
}

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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 (PSIBLAST) 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.

Keyphrases

new generation protein database search program blast program used tool gapped blast program gapped blast protein comparison gapped alignment many case sequence similarity interesting member position-specific iterated blast new heuristic position-specific score matrix significant alignment dna database weak similarity relevant sequence similarity execution time program run statistical refinement word hit new criterion

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