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FCCM
2007
IEEE

FPGA Acceleration of Gene Rearrangement Analysis

13 years 10 months ago
FPGA Acceleration of Gene Rearrangement Analysis
In this paper we present our work toward FPGA acceleration of phylogenetic reconstruction, a type of analysis that is commonly performed in the fields of systematic biology and comparative genomics. In our initial study, we have targeted a specific application that reconstructs maximum-parsimony (MP) phylogenies for gene-rearrangement data. Like other prevalent applications in computational biology, this application relies on a control-dependent, memoryintensive, and non-arithmetic combinatorial optimization algorithm. To achieve hardware acceleration, we developed an FPGA core design that implements the application’s primary bottleneck computation. Because our core is lightweight, we are able to synthesize multiple cores on a single FPGA. By using several cores in parallel, we have achieved a 25X end-to-end application speedup using simulated input data.
Jason D. Bakos
Added 02 Jun 2010
Updated 02 Jun 2010
Type Conference
Year 2007
Where FCCM
Authors Jason D. Bakos
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