Parallel Reconfigurable Operator for Genomic Sequence Comparison: Architecture and Performance Analyses

Alexandre Cornu 1 Francois Dussaugey 1 Dominique Lavenier 1
1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
Abstract : This document describes a parallel genomic sequence comparison operator for reconfigurable platforms. It has been implemented for speeding up the time consuming parts of the IRISA-TBLASTN program designed for comparing full genomes with large protein banks. Speed-up ranging from 25 to 200 has been measured on real genomic data.
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Submitted on : Tuesday, December 23, 2008 - 9:15:12 AM
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Alexandre Cornu, Francois Dussaugey, Dominique Lavenier. Parallel Reconfigurable Operator for Genomic Sequence Comparison: Architecture and Performance Analyses. [Research Report] RR-6776, INRIA. 2008. ⟨inria-00348482⟩

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