Multiple sequence alignment with evolutionary computation

Genetic Programming and Evolvable Machines

Volumn 5, Issue 2, 2004, Pages 121-144

  Shyu, Conrad ^a   Sheneman, Luke ^a   Foster, James A ^a  

^a UNIVERSITY OF IDAHO   (United States)

Author keywords

DNA sequences; Genetic algorithm; Multiple sequence alignment; Progressive alignments

Indexed keywords

DNA SEQUENCES; DYNAMIC PROGRAMMING; GRADIENT METHODS; HEURISTIC PROGRAMMING; INFORMATION ANALYSIS; LIVING SYSTEMS STUDIES; OPTIMIZATION; PROTEINS; SIGNAL ENCODING; TREES (MATHEMATICS);

MULTIPLE SEQUENCE ALIGNMENT; OPTIMAL ALIGNMENT; PROGRESSIVE ALIGNMENTS; PROTEIN SEQUENCES;

GENETIC ALGORITHMS;

EID: 3543059897     PISSN: 13892576     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:GENP.0000023684.05565.78     Document Type: Conference Paper

References (40)

1. S. F. Altschul, "Amino acid substitution matrices from an information theoretic perspective," J. of Mol. Biol. vol. 219, pp. 555-565, 1999.
2. S. F. Altschul, R. J. Carroll, and D. Lipman, "Weights for data related by a tree," J. of Mol. Biol. vol. 207, pp. 647-653, 1989.
3. S. F. Altschul and D. Lipman, "Trees, stars, and multiple sequence alignment," SIAM J. of Appl. Math. vol. 49, pp. 197-209, 1989.
4. H. Carrillo and D. Lipman, "The multiple sequence alignment problem in biology," SIAM J. of Appl. Math. vol. 48, pp. 1073-1082, 1988.
5. S. B. Carroll, J. K. Grenier, and S. D. Weatherbee, From DNA to Diversity: Molecular Genetics and the Evolutionary of Animal Designs, Maiden, MA: Blackwell Science, 2001.
6. W. H. Day and F. R. McMorris, "The computation of consensus patterns in DNA sequence," Mathematical and Computational Modul, vol. 17, pp. 49-52, 1993.
7. R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge, UK: Cambridge University, 1998.
8. D. Feng and R. F. Doolittle, "Progressive sequence alignment as a prerequisite to correct phylogenetic trees," J. of Mol. Evol. vol. 25, pp. 351-360, 1987.
9. D. B. Fogel and D. W. Come (Eds.), Evolutionary Computation in Bioinformatics, San Francisco, CA: Morgan Kaufmann Publishers, 2003.
10. D. Graur and W. H. Li, Fundamental of Molecular Evolution, 2nd ed., Sunderland, MA: Sinauer Associates, 2002.
11. D. Gusfield, Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology, New York, NY: Cambridge University Press, 1997.
12. B. G. Hall, Phylogenetics Trees Made Easy: A How-to Manual for Molecular Biologists, Sunderland, MA: Sinauer Associates, 1997.
13. J. H. Holland, Adaptation in Natural and Artificial Systems, Ann Arbor: University of Michigan Press, 1975.
14. J. T. Horng, C. M. Lin, B. J. Liu, and C. Y. Lao, "Using genetic algorithm to solve multiple sequence alignment," in Proc. Germ. Conf. on Bioinfo., E. Wingender et al. (eds.), 2001, pp. 883-890.
15. M. Isokawa, M. Wayama, and T. Shimizu, "Multiple sequence alignment using a genetic algorithm," Genome Informatics vol. 7, pp. 176-177, 1997.
16. T. H. Jukes and C. Cantor, "Evolution of protein molecules." in Mammalian Protein Metabolism M. N. Munro (ed.), New York: Academic Press, 1969, pp. 21-132.
17. K. Karadimitriou and D. H. Kraft, "Genetic algorithms and the multiple sequence alignment program in biology," in Proc. 2nd Ann. Baton Rough Area Mole. Biol. and Biotec. Conf., T. R. Tiersch et al. (eds.), 1996.
18. J. M. Keith, P. Adams, D. Bryant, D. P. Kroese, K. R. Mitchelson, D. A. E. Cochran, and G. H. Lala, "A simulated annealing algorithm for finding consensus sequences, Bioinformatics vol. 18, no. 11, pp. 1494-1499, 2002.
19. B. Morgenstern, "DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment," Bioinformatics vol. 15, no. 3, pp. 211-218, 1999.
20. S. B. Needleman and C. D. Wunsch, "A general method applicable to the search for similarities in the amino acid sequence of two proteins," J. of Mol. Biol. vol. 48, pp. 443-453, 1970.
21. C. Notredame and D. G. Higgins, "SAGA: Sequence alignment by genetic algorithm," Nucleic Acids Research vol. 24, no. 8, pp. 1515-1524, 1996.
22. C. N. S. Pedersen. "Algorithms in computational biology," Ph.D. dissertation. BRICS, Department of Computer Science, University of Aarhus, Aarhus, Denmark. March 2000.
23. A. Rambaut and N. C. Crassly, "Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees," Compu. Appl. Biosci. vol. 13, pp. 235-238, 1997.
24. N. Saitou and M. Nei, "The neighbor-joining method: A new method for reconstructing phylogenetic trees," Molecular and Biological Evolution vol 4, no. 4, pp. 406-425, 1987.
25. J. Sauder, J. Arther, and R. Dunbrack, "Large-scale of comparison of protein sequence alignment algorithms with structure alignments," Proteins: Structures, Function, and Genetics vol. 40, pp. 6-32, 2000.
26. R. E. Sean, "A memory-efficient dynamic programming algorithm for optimal alignment of sequence to an RNA secondary structure," BMC Bioinformatics vol. 3, pp. 13, 2002.
27. J. Setubal and J. Meidanis, Introduction to Computational Molecular Biology, Boston, MA: PWS Publishing, 1997.
28. T. F. Smith and M. S. Waterman, "Identification of common molecular sequences," J. of Mol. Biol. vol, 147, pp. 195-197, 1981.
29. D. J. States, W. Gish, and S. F. Altschul, "Improved sensitivity of nucleic acid database searches using application-specific scoring matrices," Methods: A Companion to Methods in Enzymology vol. 3, no. 1, pp. 66-70, 1997.
30. J. Stoye, S. W. Perry, and A. W. M. Dress, "Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment," Applied Mathematical Literature vol. 10, no. 2, pp. 67-73, 1997.
31. J. Studier and K. Keppler, "A note on the neighbor-joining algorithm of Saitou and Nei," Molecular and Biological Evolution vol. 5, pp. 729-731, 1988.
32. J. D. Thompson, T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins, "The Clustal X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools." Nucleic Acids Research vol 24, pp. 4876-4882, 1997.
33. J. D. Thompson, D. G. Higgins, and T. J. Gibson, "Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice," Nucleic Acids Research vol. 22, pp. 4673-4680, 1994.
34. J. D. Thompson, F. Plewniak, and O. Poch, "A comprehensive comparison of multiple sequence alignment programs." Nucleic Acids Research vol. 27, no. 13, pp. 2682-2690, 1999.
35. J. D. Thomson, 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.
36. L. Wang and T. Jiang, "On the complexity of multiple sequence alignment," J. of Compu. Biol. vol. 1, pp. 337-348, 1994.
37. S. M. Waterman and M. Eggert, "A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons," J. of Mol. Biol. vol. 197, pp. 723-725, 1987.
38. W. Wayama, K. Takahashi, and T. Shimizu, "An approach to amino acid sequence alignment using a genetic algorithm," Genome Informatics vol. 6, pp. 122-123, 1995.
39. D. Whitley, "A genetic algorithm tutorial," Statistics and Computing vol. 4, pp. 65-85, 1994.
40. C. Zhang and A. K. Wong, "A genetic algorithm for multiple molecular sequence alignment," Computational Applications for Biosicence. vol. 13, no. 6, pp. 565-581, 1994.