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Voss, G., Muller-Wittig, W. and Schmidt, B. (2005) Using Graphics Hardware to Accelerate Biological Sequence Database Scanning. Proceedings of the TENCON 2005—2005 IEEE Region 10 Conference, Melbourne, 21-24 November 2005, 1-6.

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

  AUTHORS: Amadou Chaibou, Oumarou Sie

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

  JOURNAL NAME: Journal of Computer and Communications, Vol.3 No.6, June 18, 2015

  ABSTRACT: 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.