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

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.

Mots clés: Parallelisation; similarity search; indexing; TBLASTN

Domaines: Architectures Matérielles [cs.AR]

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⟩