SSEARCH

See also FASTA alignment program. This is an implementation of the Smith-Waterman local alignment alignment algorithm in the FASTA package.

Speedups

The Altivec enhanced speedup makes it as fast as FASTA algorithm on PPC. An SSE speedup is also now available in the FASTA package farrar2007,farrar_web.

References

<biblio>

1. farrar2007 pmid=17110365
2. farrar_web http://farrar.michael.googlepages.com/Smith-waterman

</biblio>