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Basic local alignment search tool
October 1990
October 1990
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Abstract
A new approach to rapid sequence comparison, basic local alignment search tool (BLAST),
directly approximates alignments that optimize a measure of local similarity, the
maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties
of MSP scores allow an analysis of the performance of this method as well as the statistical
significance of alignments it generates. The basic algorithm is simple and robust;
it can be implemented in a number of ways and applied in a variety of contexts including
straightforward DNA and protein sequence database searches, motif searches, gene identification
searches, and in the analysis of multiple regions of similarity in long DNA sequences.
In addition to its flexibility and tractability to mathematical analysis, BLAST is
an order of magnitude faster than existing sequence comparison tools of comparable
sensitivity.