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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 the authors present a multiple FPGA-based Mercury BLASTN design in order to double the speed and throughput of DNA sequence computation.
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