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Using a Bio-Inspired Algorithm to Resolve the Multiple Sequence Alignment Problem

Author

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  • El-amine Zemali

    (University of Science and Technologies HouariBoumedienne (USTHB), Algiers, Algeria)

  • Abdelmadjid Boukra

    (University of Science and Technology Houari Boumediene (USTHB), Algiers, Algeria)

Abstract

One of the most challenging tasks in bioinformatics is the resolution of Multiple Sequence Alignment (MSA) problem. It consists in comparing a set of protein or DNA sequences, in aim of predicting their structure and function. This paper introduces a new bio-inspired approach to solve such problem. This approach named BA-MSA is based on Bat Algorithm. Bat Algorithm (BA) is a recent evolutionary algorithm inspired from Bats behavior seeking their prey. The proposed approach includes new mechanism to generate initial population. It consists in generating a guide tree for each solution with progressive approach by varying some parameters. The generated guide tree will be enhanced by Hill-Climbing algorithm. In addition, to deal with the premature convergence of BA, a new restart technique is proposed to introduce more diversification when detecting premature convergence. Balibase 2.0 datasets are used for experiments. The comparison with well-known methods as MSA-GA MSA-GA (w\prealign), ClustalW, and SAGA and recent method (BBOMP) shows the effectiveness of the proposed approach.

Suggested Citation

  • El-amine Zemali & Abdelmadjid Boukra, 2016. "Using a Bio-Inspired Algorithm to Resolve the Multiple Sequence Alignment Problem," International Journal of Applied Metaheuristic Computing (IJAMC), IGI Global Scientific Publishing, vol. 7(3), pages 36-55, July.
    • Handle: RePEc:igg:jamc00:v:7:y:2016:i:3:p:36-55
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