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

• 作者: Amadou Chaibou Oumarou Sie
• 来源期刊: 电脑和通信(英文)
• 学科: 工学
• 关键词: CUDA GP-GPU OPENMP PARALLEL COMPUTING Smith-Waterman
• 年，卷（期）: dnhtxyw_2015,（6）
• 页码范围: 107-117
• 页数: 11页
• 分类号: TP39

摘要

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.