%0 Journal Article %1 citeulike:238188 %A Altschul, S. F. %A Madden, T. L. %A Schäffer, A. A. %A Zhang, J. %A Zhang, Z. %A Miller, W. %A Lipman, D. J. %C National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. altschul@ncbi.nlm.nih.gov %D 1997 %J Nucleic Acids Res %K bioinformatics %N 17 %P 3389--3402 %T Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9254694 %V 25 %X 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 = {September}, 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 }