Table of Contents
Journal of Artificial Evolution and Applications
Volume 2009, Article ID 963150, 10 pages
http://dx.doi.org/10.1155/2009/963150
Research Article

Multiple Sequence Alignment Using a Genetic Algorithm and GLOCSA

1Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de Mexico, Circuito exterior s/n, Ciudad Universitaria, 04510 Mexico, DF, Mexico
2Instituto de Biología, Universidad Nacional Autónoma de Mexico, Apdo. Postal 70-367, 04510 Mexico, DF, Mexico

Received 14 November 2008; Revised 4 April 2009; Accepted 13 June 2009

Academic Editor: Jason Moore

Copyright © 2009 Edgar D. Arenas-Díaz et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. F. C. Bernstein, T. F. Koetzle, G. J. B. Williams et al., “The protein data bank: a computer based archival file for macromolecular structures,” Journal of Molecular Biology, vol. 112, no. 3, pp. 535–542, 1977. View at Google Scholar
  2. D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler, “Genbank,” Nucleic Acids Reseach, vol. 34, pp. D16–D20, 2006. View at Google Scholar
  3. R. C. Edgar, “Muscle: multiple sequence alignment with high accurracy and high throughput,” Nucleic Acids Reseach, vol. 32, no. 5, pp. 1792–1797, 2004. View at Google Scholar
  4. W. S. Klug, M. R. Cummings, and C. Spencer, Concepts of Genetics, Benjamin Cummings, Essex, UK, 2005.
  5. “Using genetic algorithms for pairwise and multiple sequence alignments,” in Evolutionary Computation in Bioinformatics, G. B. Fogel and D. W. Corne, Eds., chapter 5, Morgan Kaufman, San Francisco, Calif, USA, 2003.
  6. B. Haubold and T. Wiehe, Introduction to Computational Biology: An Evolutionary Approach, Birkhäuser, Basel, Switzerland, 2007.
  7. S. B. Needleman and C. D. Wunsch, “A general method applicable to the search for similarities in the amino acid sequence of two proteins,” Journal of Molecular Biology, vol. 48, no. 3, pp. 443–453, 1970. View at Google Scholar
  8. T. F. Smith and M. S. Waterman, “Comparison of biosequences,” Advances in Applied Mathematics, vol. 2, no. 4, pp. 482–489, 1981. View at Google Scholar
  9. M. Ishikawa, T. Toya, and Y. Tokoti, “Parallel iterative aligner with genetic algorithm,” in Proceedings of the 13th International Conference on Artificial Ingelligence and Genome Workshop, pp. 84–93, 1993.
  10. C. Notredame and D. G. Higgins, “SAGA: sequence alignment by genetic algorithm,” Nucleic Acids Research, vol. 24, no. 8, pp. 1515–1524, 1996. View at Publisher · View at Google Scholar
  11. C. Notredame, E. A. O'Brien, and D. G. Higgins, “RAGA: RNA sequence alignment by genetic algorithm,” Nucleic Acids Research, vol. 25, no. 22, pp. 4570–4580, 1997. View at Google Scholar
  12. K. Chellapilla and G. Fogel, “Multiple sequence alignment using evolutionary programming,” in Proceedings of the IEEE Congress on Evolutionary Computation, vol. 1, p. 452, Washington, DC, USA, July 1999. View at Publisher · View at Google Scholar
  13. L. Cai, D. Juedes, and E. Liakhovitch, “Evolutionary computation techniques for multiple sequence alignment,” in Proceedings of the IEEE Conference on Evolutionary Computation (ICEC '00), vol. 2, pp. 829–835, 2000.
  14. C. Sander and R. Schneider, “Database of homology-derived protein structures and the structural meaning of sequence alignment,” Proteins: Structure, Function and Genetics, vol. 9, no. 1, pp. 56–68, 1991. View at Google Scholar
  15. J. I. Davis and J. J. Doyle, “Homology in molecular phylogenetics: a parsimony perspective,” in Molecular Systematics of Plants II, pp. 101–131, Kluwer Academic Publishers, Boston, Mass, USA, 1998. View at Google Scholar
  16. H. Ochoterena, “Homology in coding and non-coding DNA sequences: a parsimony perspective,” Plant Systematics and Evolution. View at Publisher · View at Google Scholar
  17. M. O. Dayhoff, Atlas of Protein Sequence and Structure, National Biomedical Research Fundation, Washington, DC, USA, 1978.
  18. D. J. Lipman, S. F. Altschul, and J. D. Kececioglu, “A tool for multiple sequence alignment,” Proceedings of the National Academy of Sciences of the United States of America, vol. 86, no. 12, pp. 4412–4415, 1989. View at Google Scholar
  19. S. Henikoff and J. G. Henikoff, “Amino acid substitution matrices from protein blocks,” Proceedings of the National Academy of Sciences of the United States of America, vol. 89, no. 22, pp. 10915–10919, 1992. View at Publisher · View at Google Scholar
  20. S. F. Altschul, “Gap costs for multiple sequence alignment,” Journal of Theoretical Biology, vol. 138, no. 3, pp. 297–309, 1989. View at Google Scholar
  21. S. F. Altschul and D. J. Lipman, “Trees, stars, and multiple biological sequence alignment,” SIAM Journal on Applied Mathematics, vol. 49, no. 1, pp. 197–209, 1989. View at Google Scholar
  22. J. D. Thompson, F. Plewniak, and O. Poch, “BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs,” Bioinformatics, vol. 15, no. 1, pp. 87–88, 1999. View at Publisher · View at Google Scholar
  23. A. Bahr, J. D. Thompson, J.-C. Thierry, and O. Poch, “BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations,” Nucleic Acids Research, vol. 29, no. 1, pp. 323–326, 2001. View at Google Scholar