Protein similarity search with subset seeds ...
Document type :
Communication dans un congrès avec actes
Title :
Protein similarity search with subset seeds on a dedicated reconfigurable hardware
Author(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]
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]
Conference title :
Parallel Bio-Computing
City :
Gdansk,
Country :
Pologne
Start date of the conference :
2007-09-07
Publication date :
2007
English keyword(s) :
bioinformatics
subset seeds
sequence comparison
FLASH technology
FPGA
subset seeds
sequence comparison
FLASH technology
FPGA
HAL domain(s) :
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]
Informatique [cs]/Bio-informatique [q-bio.QM]
Sciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
English abstract : [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 ...
Show more >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.Show less >
Show more >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.Show less >
Language :
Anglais
Peer reviewed article :
Oui
Audience :
Internationale
Popular science :
Non
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