Journal
BIOINFORMATICS
Volume 23, Issue 2, Pages 156-161Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btl582
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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.
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