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Comparative Study of the Parallelization of the Smith-Waterman Algorithm on OpenMP and Cuda C

Amadou Chaibou, Oumarou Sie
Laboratoire de Mathematiques et Informatique (LAMI), Universite de Ouagadougou, Ouagadougou, Burkina Faso
Journal of Computer and Communications, 3, 107-117, 2015

@article{chaibou2015comparative,

   title={Comparative Study of the Parallelization of the Smith-Waterman Algorithm on OpenMP and Cuda C},

   author={Chaibou, Amadou and Sie, Oumarou},

   journal={Journal of Computer and Communications},

   volume={3},

   number={06},

   pages={107},

   year={2015},

   publisher={Scientific Research Publishing}

}

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In this paper, we present parallel programming approaches to calculate the values of the cells in matrix’s scoring used in the Smith-Waterman’s algorithm for sequence alignment. This algorithm, well known in bioinformatics for its applications, is unfortunately time-consuming on a serial computer. We use formulation based on anti-diagonals structure of data. This representation focuses on parallelizable parts of the algorithm without changing the initial formulation of the algorithm. Approaching data in that way give us a formulation more flexible. To examine this approach, we encode it in OpenMP and Cuda C. The performance obtained shows the interest of our paper.
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