A quantum evolutionary algorithm for effective multiple sequence alignment

Abstract

This paper describes a novel approach to deal with multiple sequence alignment (MSA). MSA is an essential task in bioinformatics which is at the heart of denser and more complex tasks in biological sequence analysis. MSA problem still attracts researcher's attention despite the significant research effort spent to solve it. We propose in this paper a quantum evolutionary algorithm to improve solutions given by CLUSTALX package. The contribution consists in defining an appropriate representation scheme that allows applying successfully on MSA problem some quantum computing principles like qubit representation and superposition of states. This representation scheme is embedded within an evolutionary algorithm leading to an efficient hybrid framework which achieves better balance between exploration and exploitation capabilities of the search process. Experiments on a wide range of data sets have shown the effectiveness of the proposed framework and its ability to improve by many orders of magnitude the CLUSTALX's solutions. © Springer-Verlag Berlin Heidelberg 2005.