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Bioinformatics. 2007 Jan 15;23(2):156-61. Epub 2006 Nov 16.

Striped Smith-Waterman speeds database searches six times over other SIMD implementations.

Author information

  • farrar.michael@gmail.com

Abstract

MOTIVATION:

The only algorithm guaranteed to find the optimal local alignment is the Smith-Waterman. It is also one of the slowest due to the number of computations required for the search. To speed up the algorithm, Single-Instruction Multiple-Data (SIMD) instructions have been used to parallelize the algorithm at the instruction level.

RESULTS:

A faster implementation of the Smith-Waterman algorithm is presented. This algorithm achieved 2-8 times performance improvement over other SIMD based Smith-Waterman implementations. On a 2.0 GHz Xeon Core 2 Duo processor, speeds of >3.0 billion cell updates/s were achieved.

AVAILABILITY:

http://farrar.michael.googlepages.com/Smith-waterman

PMID:
17110365
[PubMed - indexed for MEDLINE]
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