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.
Keywords
Iterated functionHeuristicSequence (biology)BiologyPosition (finance)Sequence databaseComputer scienceComputational biologyDatabaseGeneticsArtificial intelligenceMathematicsGene
Affiliated Institutions
Related Publications
Protein homology detection by HMM–HMM comparison
Abstract Motivation: Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and evolution. Results: We have gene...
DCSE, an interactive tool for sequence alignment and secondary structure research
DCSE provides a user-friendly package for the creation and editing of sequence alignments. The program runs on different platforms, including microcomputers and workstations. Ap...
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
The Catalytic Site Atlas (CSA) provides catalytic residue annotation for enzymes in the Protein Data Bank. It is available online at http://www.ebi.ac.uk/thornton-srv/databases/...
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
We define a “threaded blockset,” which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for “threaded blockset aligner...
MAFFT version 5: improvement in accuracy of multiple sequence alignment
The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i...
Publication Info
- Year
- 1997
- Type
- review
- Volume
- 25
- Issue
- 17
- Pages
- 3389-3402
- Citations
- 73388
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
73388
OpenAlex
Cite This
Stephen F. Altschul
(1997).
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic Acids Research
, 25
(17)
, 3389-3402.
https://doi.org/10.1093/nar/25.17.3389
Identifiers
- DOI
- 10.1093/nar/25.17.3389