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...
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| Veröffentlicht in: | Nucleic acids research 1997-09, Vol.25 (17), p.3389-3402 |
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| container_title | Nucleic acids research |
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| creator | Altschul, S.F Madden, T.L Schaffer, A.A Zhang, J.H Zhang, Z Miller, W Lipman, D.J |
| description | 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. |
| doi_str_mv | 10.1093/nar/25.17.3389 |
| format | Article |
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| ispartof | Nucleic acids research, 1997-09, Vol.25 (17), p.3389-3402 |
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| source | Oxford Journals Open Access Collection; MEDLINE; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Algorithms Amino Acid Sequence amino acid sequences Animals comparisons computer analysis computer software Databases, Factual DNA - chemistry gapped alignments Humans Molecular Sequence Data proteins Proteins - chemistry Sequence Alignment Software |
| title | Gapped BLAST and PSI-BLAST: a new generation of protein database search programs |
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