Titre :

Protein similarity search with subset seeds on a dedicated reconfigurable hardware

Auteur(s) :

Peterlongo, Pierre [Auteur]
Biological systems and models, bioinformatics and sequences [SYMBIOSE]
Noé, Laurent [Auteur]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Lavenier, Dominique [Auteur]
Biological systems and models, bioinformatics and sequences [SYMBIOSE]
Georges, Gilles [Auteur]
Biological systems and models, bioinformatics and sequences [SYMBIOSE]
Jacques, Julien [Auteur]
Biological systems and models, bioinformatics and sequences [SYMBIOSE]
Kucherov, Gregory [Auteur]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Giraud, Mathieu [Auteur]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]

Titre de la manifestation scientifique :

Parallel Bio-Computing

Ville :

Gdansk,

Pays :

Pologne

Date de début de la manifestation scientifique :

2007-09-07

Date de publication :

2007

Mot(s)-clé(s) en anglais :

bioinformatics
subset seeds
sequence comparison
FLASH technology
FPGA

Discipline(s) HAL :

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

Résumé en anglais : [en]

Genome sequencing of numerous species raises the need of complete genome comparison with precise and fast similarity searches. Today, advanced seed-based techniques (spaced seeds, multiple seeds, subset seeds) provide ...
Lire la suite >Genome sequencing of numerous species raises the need of complete genome comparison with precise and fast similarity searches. Today, advanced seed-based techniques (spaced seeds, multiple seeds, subset seeds) provide better sensitivity/specificity ratios. We present an implementation of such a seed-based technique onto parallel specialized hardware embedding reconfigurable architecture (FPGA), where the FPGA is tightly connected to large capacity Flash memories. This parallel system allows large databases to be fully indexed and rapidly accessed. Compared to traditional approaches like the Blastp software, we obtain both significant speed-up and better results. As our knowledge, this is the first attempt to exploit modern seed features for parallelizing similarity search.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