Comparaison intensive des séquences protéiques : indexation des banques et usage des instructions SIMD des microprocesseurs

van Hoa Nguyen 1, * Dominique Lavenier 1
* Corresponding author
1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
Abstract : This paper presents a method for speeding up the comparison of two protein banks. It is based on two techniques: bank indexing and fast computation of short alignments using the SIMD instruction set of modern microprocessors. The algorithm follows the seed-based approach in which hits are first exhibited before further processing. Performances are compared with BLASTP and show a speed-up of 4 with comparable sensitivity.
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https://hal.inria.fr/inria-00325020
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Submitted on : Thursday, September 25, 2008 - 10:49:01 PM
Last modification on : Friday, November 16, 2018 - 1:24:22 AM
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van Hoa Nguyen, Dominique Lavenier. Comparaison intensive des séquences protéiques : indexation des banques et usage des instructions SIMD des microprocesseurs. Journées Ouvertes Biologie Informatique Mathématiques - JOBIM, Jun 2008, Lille, France. ⟨inria-00325020⟩

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