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Bioinformatics Advance Access originally published online on November 16, 2006
Bioinformatics 2007 23(2):156-161; doi:10.1093/bioinformatics/btl582
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Michael Farrar


  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

Contact: farrar.michael{at}gmail.com

Associate Editor: Nikolaus Rajewsky

Received on June 22, 2006; revised on November 13, 2006; accepted on November 14, 2006

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