Bit-Parallel Multiple Pattern Matching - Inria - Institut national de recherche en sciences et technologies du numérique Access content directly
Conference Papers Year : 2011

Bit-Parallel Multiple Pattern Matching


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.
Fichier principal
Vignette du fichier
pbc11-tran.pdf (491.46 Ko) Télécharger le fichier
Origin : Files produced by the author(s)

Dates and versions

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


  • HAL Id : inria-00637227 , version 1


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⟩
248 View
742 Download


Gmail Facebook Twitter LinkedIn More