Title :
Implementing protein seed-based comparison algorithm on the SGI RASC-100 platform
Author :
Nguyen, Van-Hoa ; Cornu, Alexandre ; Lavenier, Dominique
Author_Institution :
IRISA, INRIA, Rennes, France
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.
Keywords :
biology computing; biomedical electronics; field programmable gate arrays; genomics; logic design; proteins; reconfigurable architectures; sequences; BLAST family; SGI RASC-100 accelerator; critical code section parallelization; full genomes; genomic sequence comparison algorithm; parallel FPGA; protein seed-based comparison algorithm; protein sequence; tblastn program; Assembly; Bioinformatics; Biotechnology; DNA; Data mining; Field programmable gate arrays; Genomics; Organisms; Proteins; Sequences;
Conference_Titel :
Parallel & Distributed Processing, 2009. IPDPS 2009. IEEE International Symposium on
Conference_Location :
Rome
Print_ISBN :
978-1-4244-3751-1
Electronic_ISBN :
1530-2075
DOI :
10.1109/IPDPS.2009.5161206
