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Communication Dans Un Congrès Année : 2011

Bit-Parallel Multiple Pattern Matching

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Résumé

Text matching with errors is a regular task in computational biology. We present an extension of the bit-parallel Wu-Manber algorithm to combine several searches for a pattern into a collection of fixed-length words. We further present an OpenCL parallelization of a redundant index on massively parallel multicore processors, within a framework of searching for similarities with seed-based heuristics. We successfully implemented and ran our algorithms on GPU and multicore CPU. Some speedups obtained are more than 60x.
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Dates et versions

inria-00637227 , version 1 (31-10-2011)

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  • HAL Id : inria-00637227 , version 1

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Tuan Tu Tran, Mathieu Giraud, Jean-Stéphane Varré. Bit-Parallel Multiple Pattern Matching. Parallel Processing and Applied Mathematics / Parallel Biocomputing Conference (PPAM / PBC 11), 2011, Torun, Poland. ⟨inria-00637227⟩
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