FPGA-accelerated seed generation in Mercury BLASTP

BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more runtime or a cluster of machines to keep pace. To address this problem, we have designed and built a high-performance FPGA-accelerated version of BLASTP, Mercury BLASTP. In this paper, we focus on seed generation, the first stage of the BLASTP algorithm. Our seed generator is capable of processing database residues at up to 219 Mresidues/second for 2048- residue queries. The full Mercury BLASTP pipeline, including our seed generator, achieves a speedup of 37times over the popular NCBI BLASTP software on a 2.8 GHz Intel P4 CPU, with sensitivity more than 99% that of the software. Our architecture can be generalized to accelerate the seed generation stage in other important biocomputing applications.