Fine-grained parallelization of similarity search between protein sequences

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 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.
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Submitted on : Wednesday, April 23, 2008 - 9:55:08 AM
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  • HAL Id : inria-00275250, version 2
  • ARXIV : 0804.3643

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van Hoa Nguyen, Dominique Lavenier. Fine-grained parallelization of similarity search between protein sequences. [Research Report] RR-6513, INRIA. 2008, pp.40. ⟨inria-00275250v2⟩

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