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17th IEEE International Workshop on Rapid System Prototyping (RSP'06)
Parameter-Specific FPGA Implementation of Edit-Distance Calculation
Chania, Crete
June 14-June 16
ISBN: 0-7695-2580-6
Kenneth B. Kent, University of New Brunswick, Canada
Ryan B. Proudfoot, University of New Brunswick, Canada
Yong Zhao, University of New Brunswick, Canada
Biologists require ways to rapidly sequence vast amounts of DNA information. An approach to satisfying the demand is to provide hardware support and leverage parallel computation. When providing hardware acceleration it is known that a custom specific circuit will provide a high performance solution. Providing a balance between delivering an application-specific circuit while achieving optimal utilization of a Field Programmable Gate Array is a difficult task. This paper presents a technique in which a custom circuit solution for a given parameter set is generated for the edit-distance problem in comparing two sequences for similarity.
Citation:
Kenneth B. Kent, Ryan B. Proudfoot, Yong Zhao, "Parameter-Specific FPGA Implementation of Edit-Distance Calculation," rsp, pp.209-215, 17th IEEE International Workshop on Rapid System Prototyping (RSP'06), 2006
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