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Ligowski, L. and Rudnicki, W. (2009) An Efficient Implementation of Smith Waterman Algorithm on GPU Using CUDA, for Massively Parallel Scanning of Sequence Databases. Proceedings of the 2009 IEEE International Symposium on Parallel & Distributed Processing, Rome, 23-29 May 2009, 1-8.
http://dx.doi.org/10.1109/IPDPS.2009.5160931

has been cited by the following article:

• 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.