BLAST is a widely used tool for finding matches to a query sequence within a large sequence database, such as Genbank. BLAST is designed to look for local alignments, i.e. maximal regions of high similarity between the query sequence and the database sequences, allowing for insertions and deletions of sites. Although the optimal solution to this problem is computationally intractable, BLAST uses carefully designed and tested heuristics that enable it to perform searches very rapidly (often in seconds). For each comparison, BLAST reports a goodness score and an estimate of the expected number of matches with an equal or higher score than would be found by chance, given the characteristics of the sequences. When this expected value is very small, the sequence from the database is considered a hit and a likely homologue to the query sequence. Versions of BLAST are available for protein and DNA sequences and are made accessible in MEGA via the Web Browser.
See:
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.