Author(s)

Amadou Chaibou¹, Oumarou Sie²

¹Laboratoire de Mathématiques et Informatique (LAMI), Université de Ouagadougou, Ouagadougou, Burkina Faso.
²Département de Mathmatiques et Informatique, Université de Ouagadougou, Ouagadougou, Burkina Faso.

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.

Cuda, GP-GPU, OpenMP, Parallel Computing, Smith-Waterman

Chaibou, A. and Sie, O. (2015) Comparative Study of the Parallelization of the Smith-Waterman Algorithm on OpenMP and Cuda C. Journal of Computer and Communications, 3, 107-117. doi: 10.4236/jcc.2015.36011.