Bit-Parallel Multiple Pattern Matching
Document type :
Communication dans un congrès avec actes
Title :
Bit-Parallel Multiple Pattern Matching
Author(s) :
Tran, Tuan Tu [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Giraud, Mathieu [Auteur correspondant]
Bioinformatics and Sequence Analysis [BONSAI]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Varré, Jean-Stéphane [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Bioinformatics and Sequence Analysis [BONSAI]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Giraud, Mathieu [Auteur correspondant]

Bioinformatics and Sequence Analysis [BONSAI]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Varré, Jean-Stéphane [Auteur]

Bioinformatics and Sequence Analysis [BONSAI]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Conference title :
Parallel Processing and Applied Mathematics / Parallel Biocomputing Conference (PPAM / PBC 11)
City :
Torun
Country :
Pologne
Start date of the conference :
2011
Publication date :
2011
English keyword(s) :
bit parallelism
pattern matching
sequence comparison
neighborhood indexing
GPU
OpenCL
pattern matching
sequence comparison
neighborhood indexing
GPU
OpenCL
HAL domain(s) :
Informatique [cs]/Bio-informatique [q-bio.QM]
Sciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
Sciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
English abstract : [en]
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 ...
Show more >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.Show less >
Show more >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.Show less >
Language :
Anglais
Peer reviewed article :
Oui
Audience :
Internationale
Popular science :
Non
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