Abstract
The BLAST sequence alignment program is a central application in bioinformatics. The de facto standard version, NCBI BLAST, uses complex heuristics that make it challenging to simultaneously achieve both high performance and exact agreement. We propose a system that uses novel FPGA-based filters that reduce the input database by over 99.97% without loss of sensitivity. There are several contributions. First is design of the filters themselves, which perform two-hit seeding, exhaustive ungapped alignment, and exhaustive gapped alignments, respectively. Second is the coupling of the filters, especially the two-hit seeding and the ungapped alignment. Third is pipelining the filters in a single design, including maintaining load balancing as data are reduced by orders of magnitude at each stage. Fourth is the optimization required to maintain operating frequency for the resulting complex design. And finally, there is system integration both in hardware (the Convey HC1-EX) and software (NCBI BLASTP). We present results for various usage scenarios and find complete agreement and a factor of nearly 5x speedup over a fully parallel implementation of the reference code on a contemporaneous CPU. We believe that the resulting system is the leading per-socket-accelerated NCBI BLAST.
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