June 14, 2006 to June 16, 2006
Kenneth B. Kent , University of New Brunswick, Canada
Ryan B. Proudfoot , University of New Brunswick, Canada
Yong Zhao , University of New Brunswick, Canada
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/RSP.2006.26
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.
Kenneth B. Kent, Ryan B. Proudfoot, Yong Zhao, "Parameter-Specific FPGA Implementation of Edit-Distance Calculation", RSP, 2006, Rapid System Prototyping, IEEE International Workshop on, Rapid System Prototyping, IEEE International Workshop on 2006, pp. 209-215, doi:10.1109/RSP.2006.26