inria-00275250, version 2
Fine-grained parallelization of similarity search between protein sequences
Van Hoa Nguyen
a, 1Dominique Lavenier
b, 1
N° RR-6513 (2008)
Résumé : This report presents the implementation of a protein sequence comparison algorithm specifically designed for speeding up time consuming part on parallel hardware such as SSE instructions, multicore architectures or graphic boards. Three programs have been developed: PLAST-P, TPLAST-N and PLAST-X. They provide equivalent results compared to the NCBI BLAST family programs (BLAST-P, TBLAST-N and BLAST-X) with a speed-up factor ranging from 5 to 10.
- a – INRIA
- b – CNRS
- 1 : SYMBIOSE (INRIA - IRISA)
- CNRS : UMR6074 – INRIA – INSA Rennes – Université de Rennes 1
- Domaine : Informatique/Bio-informatique
Sciences du Vivant/Bio-Informatique, Biologie Systémique - Mots-clés : Parallelization – similarity search – indexing – BLAST – GPU – SIMD
- Référence interne : RR-6513
- Versions disponibles : v1 (23-04-2008) v2 (23-04-2008)
- inria-00275250, version 2
- http://hal.inria.fr/inria-00275250
- oai:hal.inria.fr:inria-00275250
- Contributeur : Rapport De Recherche Inria
- Soumis le : Mercredi 23 Avril 2008, 09:55:08
- Dernière modification le : Jeudi 24 Avril 2008, 09:47:33
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