Hardware-Based Implementation of the Common Approximate Substring Algorithm
DSD '05 Proceedings of the 8th Euromicro Conference on Digital System Design（2005）
摘要
An implementation of an algorithm for string matching, commonly used in DNA string analysis, using configurable technology is proposed. The design of the circuit allows for pipelining to provide a performance increase. The proposal is unique in that we suggest a design that is specific to certain parameters of the problem, but may be reused for any particular instance of the problem that matches these parameters. The use of a Field Programmable Gate Array allows the implementation to be instance specific, thus ensuring maximal usage of the hardware. Analysis and preliminary results based on a prototype implementation are presented.
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关键词
performance increase,maximal usage,dna string analysis,particular instance,common approximate substring algorithm,hardware-based implementation,prototype implementation,certain parameter,configurable technology,string matching,instance specific,field programmable gate array,field programmable gate arrays,dna,logic design
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