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Implementation of Smith-Waterman Algorithm in OpenCL for GPUs

Dzmitry Razmyslovich, Guillermo Marcus, Markus Gipp, Marc Zapatka, Andreas Szillus
Inst. for Comput. Eng. (ZITI), Univ. of Heidelberg, Mannheim, Germany
Second International Workshop on Parallel and Distributed Methods in Verification, 2010 Ninth International Workshop on, and High Performance Computational Systems Biology

@conference{razmyslovich2010implementation,

   title={Implementation of Smith-Waterman Algorithm in OpenCL for GPUs},

   author={Razmyslovich, D. and Marcus, G. and Gipp, M. and Zapatka, M. and Szillus, A.},

   booktitle={2010 Ninth International Workshop on Parallel and Distributed Methods in Verification/2010 Second International Workshop on High Performance Computational Systems Biology},

   pages={48–56},

   year={2010},

   organization={IEEE}

}

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In this paper we present an implementation of the Smith-Waterman algorithm. The implementation is done in OpenCL and targets high-end GPUs. This implementation is capable of computing similarity indexes between reference and query sequences. The implementation is designed for the sequence alignment paths calculation. In addition, it is capable of handling very long reference sequences (in the order of millions of nucleotides), a requirement for the target application in cancer research. Performance compares favorably against CPU, being on the order of 9 – 130 times faster, 3 times faster than the CUDA-enabled CUDASW++v2.0 for medium sequences or larger. Additionally, it is on par with Farrar’s performance, but with less constraints in sequence length.
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