Parallelization of DNA sequence alignment using OpenMP

Authors:
S. R. Sathe;D. D. Shrimankar
Affiliations:
Visvesvaraya National Institute of Technology, Nagpur, Maharashtra, India;Visvesvaraya National Institute of Technology, Nagpur, Maharashtra, India
Venue:
Proceedings of the 2011 International Conference on Communication, Computing & Security
Year:
2011

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Abstract

In this paper, a parallel programming algorithm for DNA sequence alignment on multi-core processor architectures is proposed. We discuss the issues involved in implementation of aligning genome sequences using global sequence alignment algorithm and parallelizing them using tiling and OpenMP on multicore architecture. Sequence alignment is a fundamental instrument in Bioinformatics. In recent years, numerous proposals have been addressed the problem of accelerating this class of applications. In this paper we focus on the analysis of the alignment in global algorithm, a widely used program for performing multiple sequence alignment. We have parallelized global algorithm on multi-core architecture and have carefully analyzed the scalability of its different phases with both the number of cores used and the input size. Our experimental results illustrate that by selecting appropriate tile size for different architecture and for different input size, total parallel execution time is significantly reduced. The developed computing system is implemented on the PC-based Linux cluster with different multicore architecture.