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Bioinformatics Advance Access published online on November 16, 2006
Bioinformatics, 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
Received June 22, 2006
Revised November 13, 2006
Accepted November 14, 2006

Article

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

Michael Farrar *

* To whom correspondence should be addressed.
Michael Farrar, E-mail: farrar.michael{at}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 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 2.0GHz Xeon Core 2 Duo processor, speeds over 3.0 billion cell updates per second were achieved.

Availability: http://farrar.michael.googlepages.com/smith-waterman.

Associate Editor: Nikolaus Rajewsky
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