Pairwise sequence alignment algorithms: a survey

Authors:
Waqar Haque;Alex Aravind;Bharath Reddy
Affiliations:
University of Northern British Columbia, Prince George, BC, Canada;University of Northern British Columbia, Prince George, BC, Canada;University of Northern British Columbia, Prince George, BC, Canada
Venue:
Proceedings of the 2009 conference on Information Science, Technology and Applications
Year:
2009

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Abstract

Pairwise sequence alignment is a fundamental compute-intensive problem in bioinformatics that has helped researchers analyse biological sequences. The analysis has helped biologists detect pathogens, develop drugs, and identify common genes. The biological sequence database has been growing rapidly due to new sequences being discovered. This has brought many new challenges including sequence database searching and aligning long sequences. To solve these problems, many sequence alignment algorithms have been developed. These algorithms employ various techniques to efficiently find optimal or nearly-optimal alignments. In this paper, we present the popular past and recent work on both local and global pairwise sequence alignment algorithms. In addition to identifying the techniques used, the advantages and limitations of the algorithms are also presented.