A Parallel Non-Alignment Based Approach to Efficient Sequence Comparison using Longest Common Subsequences

Authors

Sanjukta Bhowmick, University of Nebraska at OmahaFollow
Mohammad Shafiullah, University of Nebraska at OmahaFollow
H. Rai, University of Nebraska at Omaha
Dhundy Raj Bastola, University of Nebraska at OmahaFollow

Document Type

Article

Publication Date

2010

Publication Title

Journal of Physics: Conference Series

Volume

256

Issue

012012

Abstract

Biological sequence comparison programs have revolutionized the practice of biochemistry, and molecular and evolutionary biology. Pairwise comparison of genomic sequences is a popular method of choice for analyzing genetic sequence data. However the quality of results from most sequence comparison methods are significantly affected by small perturbations in the data and furthermore, there is a dearth of computational tools to compare sequences beyond a certain length. In this paper, we describe a parallel algorithm for comparing genetic sequences using an alignment free-method based on computing the Longest Common Subsequence (LCS) between genetic sequences. We validate the quality of our results by comparing the phylogenetic tress obtained from ClustalW and LCS. We also show through complexity analysis of the isoefficiency and by empirical measurement of the running time that our algorithm is very scalable.

Comments

https://doi.org/10.1088/1742-6596/256/1/012012

Recommended Citation

Bhowmick, Sanjukta; Shafiullah, Mohammad; Rai, H.; and Bastola, Dhundy Raj, "A Parallel Non-Alignment Based Approach to Efficient Sequence Comparison using Longest Common Subsequences" (2010). Chemistry Faculty Publications. 56.
https://digitalcommons.unomaha.edu/chemfacpub/56

Creative Commons License

This work is licensed under a Creative Commons Attribution 3.0 License.