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Conference papers

Implementing Protein Seed-Based Comparison Algorithm on the SGI RASC-100 Platform

van Hoa Nguyen 1, * Alexandre Cornu 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 paper describes a parallel FPGA implementation of a genomic sequence comparison algorithm for finding similarities between a large set of protein sequences and full genomes. Results comparable to the tblastn program from the BLAST family are provided while the computation is improved by a factor 19. The performances are mainly due to the parallelization of a critical code section on the SGI RASC-100 accelerator.
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Submitted on : Tuesday, October 20, 2009 - 4:08:55 PM
Last modification on : Friday, February 4, 2022 - 3:15:21 AM
Long-term archiving on: : Wednesday, June 16, 2010 - 12:56:04 AM


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  • HAL Id : inria-00425237, version 1


van Hoa Nguyen, Alexandre Cornu, Dominique Lavenier. Implementing Protein Seed-Based Comparison Algorithm on the SGI RASC-100 Platform. Reconfigurable Architectures Workshop - IPDPS, May 2009, Rome, Italy. ⟨inria-00425237⟩



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