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Parallel Implementation of the Wu-Manber Algorithm Using the OpenCL Framework

Themistoklis K. Pyrgiotis, Charalampos S. Kouzinopoulos, Konstantinos G. Margaritis
Parallel and Distributed Processing Laboratory, Department of Applied Informatics, University of Macedonia, 156 Egnatia str., P.O. Box 1591, 54006 Thessaloniki, Greece
Artificial Intelligence Applications and Innovations (AIAI), 2012
@article{pyrgiotis2012parallel,

   title={Parallel Implementation of the Wu-Manber Algorithm Using the OpenCL Framework},

   author={Pyrgiotis, Themistoklis K. and Kouzinopoulos, Charalampos S. and Margaritis, Konstantinos G.},

   year={2012}

}

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One of the most significant issues of the computational biology is the multiple pattern matching for locating nucleotides and amino acid sequence patterns into biological databases. Sequential implementations for these processes have become inadequate, due to an increasing demand for more computational power. Graphic cards offer a high parallelism computational power improving the performance of applications. This paper evaluates the performance of the Wu-Manber algorithm implemented with the OpenCL framework, by presenting the running time of the experiments compared with the corresponding sequential time.
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