Gene

Algorithm

Biology

Alignment-free sequence analysis

Statistics

Similarity (geometry)

Data mining

Computer science

Computational biology

Genetics

Sequence (biology)

Mathematics

Image (mathematics)

Similitude

Multiple sequence alignment

Artificial intelligence

Measure (data warehouse)

Sequence alignment

Flexibility (engineering)

Peptide sequence

Smith–Waterman algorithm

Journal of Molecular Biology

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.

Basic local alignment search tool.