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.