PLAST: parallel local alignment search tool for database comparison

Van Hoa Nguyen 1, * Dominique Lavenier 1, *
* Auteur correspondant
1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
Abstract : Sequence similarity searching is an important and challenging task in molecular biology and next-generation sequencing should further strengthen the need for faster algorithms to process such vast amounts of data. At the same time, the internal architecture of current microprocessors is tending towards more parallelism, leading to the use of chips with two, four and more cores integrated on the same die. The main purpose of this work was to design an effective algorithm to fit with the parallel capabilities of modern microprocessors. A parallel algorithm for comparing large genomic banks and targeting middle-range computers has been developed and implemented in PLAST software. The algorithm exploits two key parallel features of existing and future microprocessors: the SIMD programming model (SSE instruction set) and the multithreading concept (multicore). Compared to multithreaded BLAST software, tests performed on an 8-processor server have shown speedup ranging from 3 to 6 with a similar level of accuracy. A parallel algorithmic approach driven by the knowledge of the internal microprocessor architecture allows significant speedup to be obtained while preserving standard sensitivity for similarity search problems.
Type de document :
Article dans une revue
BMC Bioinformatics, BioMed Central, 2009, 10, pp.24
Liste complète des métadonnées
Contributeur : Van Hoa Nguyen <>
Soumis le : mardi 20 octobre 2009 - 17:36:53
Dernière modification le : vendredi 16 novembre 2018 - 01:21:55
Document(s) archivé(s) le : mardi 15 juin 2010 - 21:35:55


Fichiers produits par l'(les) auteur(s)


  • HAL Id : inria-00425301, version 1


Van Hoa Nguyen, Dominique Lavenier. PLAST: parallel local alignment search tool for database comparison. BMC Bioinformatics, BioMed Central, 2009, 10, pp.24. 〈inria-00425301〉



Consultations de la notice


Téléchargements de fichiers