Abstract
Approximate pattern matching (APM) is commonly used in bioinformatics, network security and information retrieval to find a pattern from a large database. Unlike exact pattern matching, APM allows limited number of errors in search process. Bit-parallel APM represents the internal states as bit value, then utilizes the bit-level parallelism to speed up the pattern matching process. One of the notable examples is Wu-Manber algorithm that enjoy great speed performance in parallel hardware accelerator like GPU and Xeon Phi. In this paper, we extend the Wu-Manber implementation in GPU to achieve faster pattern matching speed for small patterns on various state of the art GPU platforms. The experimental results show that our proposed technique can improve the pattern matching speed by 3.32% – 17.15% for short patterns on K40c, GTX980 and GTX1080 respectively.
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