publication . Article . Other literature type . 1997

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

Altschul, S F; Madden, T L; Schäffer, A A; Zhang, J; Zhang, Z; Miller, W; Lipman, D J;
Open Access
  • Published: 01 Sep 1997 Journal: Nucleic Acids Research, volume 25, pages 3,389-3,402 (eissn: 1362-4962, Copyright policy)
  • Publisher: Oxford University Press (OUP)
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 ...
Subjects
Medical Subject Headings: hemic and lymphatic diseases
ACM Computing Classification System: ComputingMethodologies_PATTERNRECOGNITION
free text keywords: Gap penalty, Sequence database, Structural Classification of Proteins database, CDNA Subtraction, Smith–Waterman algorithm, Bioinformatics, Sequence profiling tool, BLOSUM, Substitution matrix, Biology, Research Article
Related Organizations
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 ...
Subjects
Medical Subject Headings: hemic and lymphatic diseases
ACM Computing Classification System: ComputingMethodologies_PATTERNRECOGNITION
free text keywords: Gap penalty, Sequence database, Structural Classification of Proteins database, CDNA Subtraction, Smith–Waterman algorithm, Bioinformatics, Sequence profiling tool, BLOSUM, Substitution matrix, Biology, Research Article
Related Organizations
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