Efficient Parallel Design for Edit distance algorithm in DNA Sequence Alignment

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Xu Li 1 Zhenzhou Ji 1

1. Department of Computer Science and Engineering, Harbin Institute of Technology, 150001 Harbin, China

* Corresponding author.

DOI: https://doi.org/10.5815/ijem.2011.04.05

Received: 4 May 2011 / Revised: 14 Jun. 2011 / Accepted: 21 Jul. 2011 / Published: 29 Aug. 2011

Index Terms

Bioinformatics, sequence alignment, Needleman-Wunsch, Edit Distance, parallel design


The focus of Bioinformatics research is usually on two aspects—genomics and proteomics, specifically, it’s starting from nucleic acid and protein sequences, analyzing the structural and functional biological information expressed in the sequences. Biological sequence alignment is one of the common problems, the Needleman-Wunsch algorithm based on dynamic programming is the most basic algorithm, and Edit Distance(Levenshtein Distance) algorithm is also widely used in DNA sequence alignment. Nowadays, there are large amount of improvements on the Needleman-Wunsch algorithm, while few on Edit Distance algorithm, so this paper focuses on revealing the effects of parallel design on optimizing the Edit Distance algorithm, and it also compares the two algorithms’ different significances in DNA sequence alignment objectively.

Cite This Paper

Xu Li,Zhenzhou Ji,"Efficient Parallel Design for Edit distance algorithm in DNA Sequence Alignment", IJEM, vol.1, no.4, pp.32-38, 2011. DOI: 10.5815/ijem.2011.04.05


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