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

M. Farrar
Bioinformatics (Oxford, England), Vol. 23, No. 2. (15 January 2007), pp. 156-161

@article{farrar2007striped,

   title={Striped Smith–Waterman speeds database searches six times over other SIMD implementations},

   author={Farrar, M.},

   journal={Bioinformatics},

   volume={23},

   number={2},

   pages={156},

   year={2007},

   publisher={Oxford Univ Press}

}

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