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.
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