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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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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