Implementing protein seed-based comparison algorithm on the SGI RASC-100 platform

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.

• Type: Conference
• Year: 2009
• Where: IPPS
• Authors: Van Hoa Nguyen, Alexandre Cornu, Dominique Lavenier
• Keywords: Distributed And Parallel Computing, Genomic Sequence Comparison, IPPS 2009, Parallel Fpga Implementation, SGI RASC-100 Accelerator