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

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 ID: 9254694


  • Altschul SF
  • Madden TL
  • Schäffer AA
  • Zhang J
  • Zhang Z
  • Miller W
  • Lipman DJ


Nucleic acids research

Publication Data

September 1, 1997

Associated Grants

  • Agency: NLM NIH HHS, Id: LM05110

Mesh Terms

  • Algorithms
  • Amino Acid Sequence
  • Animals
  • DNA
  • Databases, Factual
  • Humans
  • Molecular Sequence Data
  • Proteins
  • Sequence Alignment
  • Software