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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 [1, 2].

References

  1. Farrar M. Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinformatics. 2007 Jan 15;23(2):156-61. DOI:10.1093/bioinformatics/btl582 | PubMed ID:17110365 | HubMed [farrar2007]
  2. http://farrar.michael.googlepages.com/Smith-waterman [farrar_web]
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