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Most Cited Journal Articles 2005-Chemistry and Related

Following is a CAS database record representing a highly cited journal article.

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CAS subject entries for this document include: Algorithm; Computer program; DNA sequences; and 3 additional concepts.

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TITLE:	Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
AUTHOR(S):	Altschul, Stephen F.; Madden, Thomas L.; Schaffer, Alejandro A.; Zhang, Jinghui; Zhang, Zheng; Miller, Webb; Lipman, David J.
CORPORATE SOURCE:	Natl. Cent. Biotechnol. Information, Natl. Library Med., Natl. Inst. Health, Bethesda, MD, 20894, USA
SOURCE:	Nucleic Acids Research (1997), 25(17), 3389-3402 CODEN: NARHAD; ISSN: 0305-1048
PUBLISHER:	Oxford University Press
LANGUAGE:	English

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 approx. three times the speed of the original. In addn., 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 approx. the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biol. relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily. The source code for the new BLAST programs is available by anonymous ftp from the machine ncbi.nlm.nih.gov, within the directory 'blast', and the programs may be run from NCBIs web site at http://www.ncbi.nlm.nih.gov/.