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

@article{Altschul1997, 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.}, 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.}, citeulike-article-id = {238188}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/25.17.3389}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/25/17/3389}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/9254694}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=9254694}, day = {1}, doi = {10.1093/nar/25.17.3389}, issn = {0305-1048}, journal = {Nucleic acids research}, keywords = {blast, method}, month = {September}, number = {17}, pages = {3389--3402}, posted-at = {2009-07-05 05:40:33}, priority = {2}, title = {Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.}, url = {http://dx.doi.org/10.1093/nar/25.17.3389}, volume = {25}, year = {1997} }

TY - JOUR ID - Altschul1997 L3 - citeulike-article-id:238188 N2 - 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. IS - 17 JF - Nucleic acids research SN - 0305-1048 AD - National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. altschul@ncbi.nlm.nih.gov EP - 3402 TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. VL - 25 SP - 3389 KW - blast KW - method AU - Altschul, SF AU - Madden, TL AU - Schäffer, AA AU - Zhang, J AU - Zhang, Z AU - Miller, W AU - Lipman, DJ PY - 1997/09/01/ UR - http://dx.doi.org/10.1093/nar/25.17.3389 ER -