Title: RBT-L: A location based approach for solving the Multiple Sequence Alignment problem

Authors: Javid Taheri, Albert Y. Zomaya

Addresses: School of Information Technologies, J12, The University of Sydney, Sydney, NSW 2006, Australia. ' School of Information Technologies, J12, The University of Sydney, Sydney, NSW 2006, Australia

Abstract: This paper presents a novel approach to solve the Multiple Sequence Alignment (MSA) problem. The Rubber Band Technique: Location Base (RBT-L) introduced in this paper, is inspired by the elastic behaviour of a Rubber Band (RB) on a plate with poles. RBT-L is an iterative optimisation algorithm designed and implemented to find the optimal alignment for a set of input protein sequences. RBT-L is tested with one of the well-known benchmarks (BALiBASE 2.0) in this field. The obtained results show the superiority of the proposed technique even in the case of formidable sequences.

Keywords: algorithms; MSA; multiple sequence alignment; optimisation; bioinformatics; rubber bands; elasticity; protein sequences.

DOI: 10.1504/IJBRA.2010.031291

International Journal of Bioinformatics Research and Applications, 2010 Vol.6 No.1, pp.37 - 57

Published online: 27 Jan 2010 *

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