Technical Report Number
Biosequence similarity search is an important application in computational biology. Mercury BLASTN, an FPGA-based implementation of BLAST for DNA, is one of the alternatives for fast DNA sequence comparison. The re-design of BLAST into a streaming application combined with a high-throughput hardware pipeline have enabled Mercury BLAST to emerge as one of the fastest implementations of bio-sequence similarity search. This performance can be further enhanced by exploiting the data-level parallelism present within the application. Here we present a multiple FPGA-based Mercury BLASTN design in order to double the speed and throughput of DNA sequence computation. This paper describes a dual Mercury BLASTN design, the detailed design of the split and merge functions, and simulation results.
Ahir, Jwalant; Buhler, Jeremy; and Chamberlain, Roger D., "Split and Merge Functions for Supporting Multiple Processing Pipelines in Mercury BLASTN" Report Number: WUCSE-2010-23 (2010). All Computer Science and Engineering Research.