A Banded Smith-Waterman FPGA Accelerator for Mercury BLASTP

Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. The popular BLASTP software for this task has become a bottleneck for proteomic database search. One third of this software's time is spent executing the Smith-Waterman dynamic programming algorithm. This work describes a novel FPGA design for banded Smith-Waterman, an algorithmic variant tuned to the needs of BLASTP. This design has been implemented in Mercury BLASTP, our FPGA-accelerated version of the BLASTP algorithm. We show that Mercury BLASTP runs 6-16 times faster than software BLASTP on a modern CPU while delivering 99% identical results.