Seed-based genomic sequence comparison using a FPGA/FLASH accelerator

This paper presents a parallel architecture for computing genomic sequence alignments using seed-based algorithms. Originality comes from the simultaneous use of FPGA components and flash memories. The FPGA technology brings the computer power while the flash memory provides high memory bandwidth able to feed a large array of specific operators. A 64 GBytes flash memory connected to a Xilinx Virtex-2 Pro PCI board has been developed and an array of 160 distance-computation operators have been implemented to perform the first step of seed-based alignment algorithms. Compared to the blast reference software family, we measured a speed-up of 75 on a real intensive genomic sequence comparison application