FPGA-based BLAST prefiltering

BLAST, the most widely used bioinformatics search tool, is routinely used for tasks infeasible to run on commodity computer systems. Prefiltering appears to be a promising acceleration approach that conserves the behavior of the original program yet provides significant search speedup. We conceived and implemented one such prefilter system based on FPGA accelerator technology. Our results indicate that our system may prove to be a viable BLAST accelerator solution.