Mercury BLASTN: Faster DNA Sequence Comparison using a Streaming Hardware Architecture

Motivation: Large-scale DNA sequence comparison, as implemented by BLAST and related algorithms, is one of the pillars of modern genomic analysis. One way to accelerate these computations is with a streaming architecture, in which processors are arranged in a pipeline that replicates the multistage structure of the algorithm. To achieve high performance, the processor hardware implementing the critical seed matching and ungapped extension stages of BLAST should be specialized to execute these stages as quickly as possible. However, accelerating these stages requires solving two key problems: first, the seed matching stage is not of a form which has traditionally been amenable to hardware acceleration; and second, the accelerated implementation of BLAST should retain sensitivity at least comparable to that of the original software. Results: We describe Mercury BLASTN, an FPGA-based implementation of BLAST for DNA. Mercury BLASTN combines a Bloom filtering approach to seed matching with a modified ungapped extension algorithm to overcome barriers to placing the early stages of BLAST onto hardware. On a previous-generation FPGA hardware platform, Mercury BLASTN runs 5 to 11 times faster than NCBI BLASTN current-generation general-purpose CPUs, with the prospect of a further eight-fold speedup on current-generation FPGAs. Moreover, its sensitivity to significant DNA sequence alignments is 99% of that observed with software NCBI BLASTN. Availability: Academic users should contact the authors for information on acquiring a prototype of the Mercury BLASTN system. Contact: [email protected]