Abstract
In view of the problem that the genetic algorithm is easy to fall into local optimization and converge slowly at the later stage of multiple sequence alignment, we propose a multigroup parallel genetic algorithm. We utilize the methods of multigroup parallel and migration strategy, and design a new mutation operator, which enhance its ability to achieve good quality solutions. Then some sequences are chosen from the BALIBASE database 1.0 as test data and the experiment results show the effectiveness of our method.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Guan, W.H., Xu, Z.Y., Zhu, P.: Nonlinear prediction analysis of properties in protein sequences. Journal of Food Science and Biotechnology 27, 71–75 (2008)
Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology 48, 443–453 (1970)
Hogeweg P. Hesper B. The alignment of sets of sequences and the construction of phylogenetic trees: An integrated method. Journal of Molecular Evolution. 20, 175–18 (1984)
Feng, D.F., Doolittle, R.F.: Progressive sequence alignment as a prerequisite to correct phylogenetic trees. Journal of Molecular Evolution 25, 351–360 (1987)
Taylor, W.R.: A flexible method to align large numbers of biological sequences. Journal of Molecular Evolution 28, 161–169 (1988)
Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTALX: improving the sensitivity of progressive multiple sequence alignment through sequence weighting position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4468–4673 (1944)
Notredame, C., Higgins, D.G.: SAGA: sequence alignment by genetic alignment. Nucleic Acids Research 24, 1515–1524 (1996)
Krogh, A., Brown, M., Mian, I.S., Sjolander, K., Haussler, D.: Hidden Markov models in computational biology. Applications to protein modeling. J. Mol. Biol. 235, 1501–1531 (1994)
Motredama, B.: DIALIGN2: improvement of the segment to segment approach to multiple sequence alignment. Bioinformatics 15, 211–218 (1999)
Notredame, C., Holm, L., Higgins, D.G.: COFFEE: An objective function for multiple sequence alignment. Bioinformatics 14, 407–422 (1998)
Huo, H., Stojkovic, V., Xie, Q.: A quantum-inspired genetic algorithm based on probabilistic coding for multiple sequence alignment. Journal of Bioinformatics and Computational Biology 1, 59–75 (2010)
Thomsen, R., Fogel, G.B., Krink, T.: A Clustal Alignment Improver using Evolutionary Algorithms. In: Proceedings of the Fourth Congress on Evolutionary Computation, vol. 1, pp. 121–126 (2002)
Huo, H., Stojkovic, V.: Two-Phase Quantum Based Evolutionary Algorithm for Multiple Sequence Alignment. In: Wang, Y., Cheung, Y.-m., Liu, H. (eds.) CIS 2006. LNCS (LNAI), vol. 4456, pp. 11–21. Springer, Heidelberg (2007)
Matsumura, T., Nakamura, M., Okech, J., et al.: A parallel and distributed genetic algorithm on loosely-coupled multiprocessor system. IEICE Trans Fundam. Electron. Commun. Comput. Sci. E81A(4), 540–546 (1998)
Notredame, C., Higgins, D.G., Heringa, J.: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205–217 (2000)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Luo, J., Zhang, L., Liang, C. (2011). A Multigroup Parallel Genetic Algorithm for Multiple Sequence Alignment. In: Deng, H., Miao, D., Lei, J., Wang, F.L. (eds) Artificial Intelligence and Computational Intelligence. AICI 2011. Lecture Notes in Computer Science(), vol 7002. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-23881-9_41
Download citation
DOI: https://doi.org/10.1007/978-3-642-23881-9_41
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-23880-2
Online ISBN: 978-3-642-23881-9
eBook Packages: Computer ScienceComputer Science (R0)