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. Nucleic Acids Res, 25(17):3389–3402, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. altschul@ncbi.nlm.nih.gov, 09, 1997. ![Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper abstract bibtex 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.
@article{citeulike:238188,
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.},
added-at = {2007-02-02T11:54:15.000+0100},
address = {National Center for Biotechnology Information, National Library of
Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
altschul@ncbi.nlm.nih.gov},
author = {Altschul, S. F. and Madden, T. L. and Sch{\"{a}}ffer, A. A. and Zhang, J. and Zhang, Z. and Miller, W. and Lipman, D. J.},
biburl = {https://www.bibsonomy.org/bibtex/27191aa4e12e0339588023211f3bcadba/robert},
citeulike-article-id = {238188},
interhash = {8f1be2202d2400934b950297852032d4},
intrahash = {7191aa4e12e0339588023211f3bcadba},
issn = {0305-1048},
journal = {Nucleic Acids Res},
keywords = {bioinformatics},
month = {09},
number = 17,
pages = {3389--3402},
priority = {2},
timestamp = {2007-02-02T11:54:15.000+0100},
title = {Gapped BLAST and PSI-BLAST: a new generation of protein database
search programs.},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=pubmed\&dopt=Abstract\&list_uids=9254694},
volume = 25,
year = 1997
}
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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. 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