Fine-grained parallelization of similarity search between protein sequences

van Hoa Nguyen (1) , Dominique Lavenier (1)

1 SYMBIOSE - Biological systems and models, bioinformatics and sequences

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.

Mots clés: Parallelization; similarity search; indexing; BLAST; GPU; SIMD

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

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