Titre :

Bit-Parallel Multiple Pattern Matching

Auteur(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]

Titre de la manifestation scientifique :

Parallel Processing and Applied Mathematics / Parallel Biocomputing Conference (PPAM / PBC 11)

Ville :

Torun

Pays :

Pologne

Date de début de la manifestation scientifique :

2011

Date de publication :

2011

Mot(s)-clé(s) en anglais :

bit parallelism
pattern matching
sequence comparison
neighborhood indexing
GPU
OpenCL

Discipline(s) HAL :

Informatique [cs]/Bio-informatique [q-bio.QM]
Sciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]

Résumé en anglais : [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 ...
Lire la suite >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.Lire moins >

Langue :

Anglais

Comité de lecture :

Oui

Audience :

Internationale

Vulgarisation :

Non

Collections :

• Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL