TSGA-MSA: Trace Sequence Algorithm for Alignment of MSA

Multiple sequence alignment (MSA) is an NP-complete and important problem in bioinformatics. In this paper, we have proposed iterative alignment method using a Genetic Algorithm for Multiple Sequence Alignment, named TSGAMSA. The steps in this algorithm are discussed in details and its performances on a set of benchmark datasets from the BAliBase 2.0 are analysed. The experimental results, the effects of the initial generation and genetic operators on the performance of this algorithm, the parameter settings, and a comparison of results with other well-known algorithm are presented and discussed.

[1]  I. O. Akinyemi,et al.  Aligning Multiple Sequences with Genetic Algorithm , 2009 .

[2]  Mohamed Batouche,et al.  Multiple sequence alignment by quantum genetic algorithm , 2006, Proceedings 20th IEEE International Parallel & Distributed Processing Symposium.

[3]  Andrew K. C. Wong,et al.  Toward efficient multiple molecular sequence alignment: a system of genetic algorithm and dynamic programming , 1997, IEEE Trans. Syst. Man Cybern. Part B.

[4]  Shane S. Sturrock,et al.  Time Warps, String Edits, and Macromolecules – The Theory and Practice of Sequence Comparison . David Sankoff and Joseph Kruskal. ISBN 1-57586-217-4. Price £13.95 (US$22·95). , 2000 .

[5]  R. Abdullah,et al.  Multiple sequence alignment using genetic algorithm and simulated annealing , 2004, Proceedings. 2004 International Conference on Information and Communication Technologies: From Theory to Applications, 2004..

[6]  C. Notredame,et al.  Recent progress in multiple sequence alignment: a survey. , 2002, Pharmacogenomics.

[7]  Olivier Poch,et al.  BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations , 2001, Nucleic Acids Res..

[8]  Liisa Holm,et al.  COFFEE: an objective function for multiple sequence alignments , 1998, Bioinform..

[9]  D. Higgins,et al.  SAGA: sequence alignment by genetic algorithm. , 1996, Nucleic acids research.

[10]  David Sankoff,et al.  Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison , 1983 .

[11]  Liming Cai,et al.  Evolutionary computation techniques for multiple sequence alignment , 2000, Proceedings of the 2000 Congress on Evolutionary Computation. CEC00 (Cat. No.00TH8512).

[12]  Miguel A. Vega-Rodríguez,et al.  An evolutionary approach for performing multiple sequence alignment , 2010, IEEE Congress on Evolutionary Computation.

[13]  Kotaro Hirasawa,et al.  Multiple Sequence Alignment Based on Genetic Algorithms with Reserve Selection , 2008, 2008 IEEE International Conference on Networking, Sensing and Control.

[14]  Hamid Beigy,et al.  A New Genetic Algorithm for Multiple sequence Alignment , 2012, Int. J. Comput. Intell. Appl..

[15]  Ying-Tung Hsiao,et al.  A novel GA-based algorithm approach to fast biosequence alignment , 2004, IEEE Conference on Cybernetics and Intelligent Systems, 2004..

[16]  V. Sundararajan,et al.  Multiple Sequence Alignment Using Parallel Genetic Algorithms , 1998, SEAL.

[17]  Yi Pan,et al.  Multiple Sequence Alignment by Ant Colony Optimization and Divide-and-Conquer , 2006, International Conference on Computational Science.

[18]  Héctor Pomares,et al.  Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns , 2013, Bioinform..

[19]  Li-fang Liu,et al.  Aligning multiple sequences by genetic algorithm , 2004, 2004 International Conference on Communications, Circuits and Systems (IEEE Cat. No.04EX914).

[20]  Gary B. Fogel,et al.  Improvement of clustal-derived sequence alignments with evolutionary algorithms , 2003, The 2003 Congress on Evolutionary Computation, 2003. CEC '03..

[21]  Moritoshi Yasunaga,et al.  Improved GA-based method for multiple protein sequence alignment , 2003, The 2003 Congress on Evolutionary Computation, 2003. CEC '03..