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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:8353 - 85 self
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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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