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Erschienen in:
2011 | OriginalPaper | Buchkapitel
Fast and Accurate Similarity Searching of Biopolymer Sequences with GPU and CUDA
verfasst von : Robert Pawłowski, Bożena Małysiak-Mrozek, Stanisław Kozielski, Dariusz Mrozek
Erschienen in: Algorithms and Architectures for Parallel Processing
Verlag: Springer Berlin Heidelberg
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CUDA is an architecture introduced by NVIDIA Corporation, which allows software developers to take advantage of GPU resources in order to increase the computational power. This paper presents an approach to accelerate the similarity searching of DNA and protein molecules through parallel alignments of their sequences with the use of GPU and CUDA. In order to optimally align two biopolymer sequences, such as amino acid or nucleotide sequences, we employ the Smith-Waterman algorithm. We present the optimization steps leading to achieve a very good efficiency of our implementation on GPU and we compare results of efficiency tests with other known implementations. The results show that it is possible to search bioinformatics databases accurately within a reasonable time.