Fine-grained parallelization of similarity search between protein sequencesReport as inadecuate

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* 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.

Keywords : Parallelization similarity search indexing BLAST GPU SIMD

Author: Van Hoa Nguyen - Dominique Lavenier -



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