inria-00275250, version 2
Fine-grained parallelization of similarity search between protein sequences
Van Hoa Nguyen
a, 1Dominique Lavenier
b, 1
N° RR-6513 (2008)
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.
- a – INRIA
- b – CNRS
- 1: SYMBIOSE (INRIA - IRISA)
- CNRS : UMR6074 – INRIA – INSA Rennes – Université de Rennes 1
- Domain : Computer Science/Bioinformatics
Life Sciences/Quantitative Methods - Keywords : Parallelization – similarity search – indexing – BLAST – GPU – SIMD
- Internal note : RR-6513
- Available versions : v1 (2008-04-23) v2 (2008-04-23)
- inria-00275250, version 2
- http://hal.inria.fr/inria-00275250
- oai:hal.inria.fr:inria-00275250
- From: Rapport De Recherche Inria
- Submitted on: Wednesday, 23 April 2008 09:55:08
- Updated on: Thursday, 24 April 2008 09:47:33
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