Toward efficient multiple molecular sequence alignment: A system of genetic algorithm and dynamic programming

IEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics

Volumn 27, Issue 6, 1997, Pages 918-932

  Zhang, Ching ^b   Wong, Andrew K C ^a,b  

^a IEEE

^b UNIVERSITY OF WATERLOO   (Canada)

Author keywords

Biomolecular sequence alignment; Dynamic programming; Genetic algorithm; Multiple sequence alignment

Indexed keywords

COMPUTATIONAL COMPLEXITY; DYNAMIC PROGRAMMING; GENETIC ALGORITHMS;

MOLECULAR SEQUENCE ALIGNMENT;

MOLECULAR ORIENTATION;

EID: 0031357475     PISSN: 10834419     EISSN: None     Source Type: Journal    
DOI: 10.1109/3477.650054     Document Type: Article

References (38)

1. C. A. Ankenbrandt, "An extension to the theory of convergence and a proof of the time complexity of genetic algorithms," in Foundations of Genetic Algorithms, G. J. E. Rawlins, Ed. San Mateo, CA: Morgan Kaufmann, 1991, pp. 53-68.
2. F. H. D. van Batenbury, A. P. Gultyaev, and C. W. A. Pleij, "An APL-programmed genetic algorithm for the prediction of RNA secondary structure," J. Theor. Biol., vol. 174, pp. 269-280, 1995.
3. S. C. Chan, "A hierarchical sequence synthesis procedure," Ph.D. dissertation, Univ. Waterloo, Waterloo, Ont., Canada, 1990.
4. S. C. Chan, A. K. C. Wong, and D. K. Y. Chiu, "A survey of multiple sequence comparison methods," Bull. Math. Biol., vol. 54, pp. 563-598, 1992.
5. T. Dandekar and P. Argos, "Potential of genetic algorithms in protein folding and protein engineering simulations," Protein Eng., vol. 5, no. 7, pp. 637-545, 1992.
6. K. De Jong, "Learning with genetic algorithms: An overview," in Machine Learning 3. Hingham, MA: Kluwer, 1988, pp. 121-138.
7. D. F. Feng, M. S. Johnson, and R. F. Doolittle, "Aligning amino acid sequences: Comparison of commonly used methods," J. Mol. Evolution, vol. 21, pp. 112-125, 1985.
8. D. F. Feng and R. F. Doolittle, "Progressive sequence alignment as prerequisite to correct phylogenetic trees," J. Mol. Evolution, vol. 25, pp. 351-360, 1987.
9. D. E. Goldberg, "Simple genetic algorithms and the minimal, deceptive problem," Genetic Algorithms and Simulated Annealing, L. Davis, Ed. London, U.K.: Pitman, 1987, pp. 74-88.
10. _, Genetic Algorithms in Search, Optimization, and Machine Learning. New York: Addison-Wesley, 1989.
11. _, "Sizing populations for serial and parallel algorithms," in Proc. 3rd Int. Conf. Genetic Algorithms. San Mateo, CA: Morgan Kaufmann, 1989, pp. 70-79.
12. O. Gotoh, "An improved algorithm for matching biological sequences," J. Mol. Biology, vol. 162, pp. 705-708, 1982.
13. _, "Consistency of optimal sequence alignments," Bull. Math. Biol., vol. 52, pp. 509-525, 1990.
14. J. J. Grefenstette and J. M. Fitzpatrick, "Genetic search with approximate function evaluations," in Proc. Int. Conf. Genetic Algorithms Applications. Hillsdale, NJ: Lawrence Erlbaum, 1985, pp. 112-120.
15. J. J. Grefenstette, "Optimization of control parameters for genetic algorithms," IEEE Trans. Syst., Man, Cybern., vol. SMC-16, no. 1, pp. 122-128, 1986.
16. J. R. Griggs, P. J. Hanlon, and M. S. Waterman "On the number of alignments of k sequences," Asian J. Comb., 1989.
17. A. P. Gultyaev, F. H. D. V. Batenbury, and C. W.A. Pleij, "The influence of a metastable structure in plasmid primer RNA on antisence RNA binding kinetics," Nucleic Acids Res., vol. 23, no. 18, pp. 3718-3725, 1995.
18. D. Gusfield, "Efficient methods for multiple sequence alignment with guaranteed error bounds," Bull. Math. Biol., vol. 55, pp. 141-154, 1993.
19. D. S. Hirschberg, "A linear space algorithm for computing longest common subsequences," Commun. Assoc. Comput. Mach., vol. 18, pp. 341-343, 1975.
20. J. H. Holland, Adoption in Natural and Artificial Systems. Ann Arbor, MI: Univ. Michigan Press, 1975.
21. _, "Escaping brittleness: The possibilities of general-purpose learning algorithms applied to parallel rule-based systems," in Machine Learning: An Artificial Intelligence Approach, Michalski et al., Eds. San Mateo, CA: Morgan Kaufmann, 1986, vol. 2, pp. 593-623.
22. _, "Genetic algorithms and classifier systems: foundations and future directions," Genetic Algorithms Their Applications: Proc. 2nd Int. Conf. Genetic Algorithms. Hillsdale, NJ: Lawrence Erlbaum, 1987, pp. 82-89.
23. D. Jeanteur, J. H. Lakey, and F. Pattus, "The bacterial porin superfamily: Sequence alignment and structure prediction," Mol. Microbiology, vol. 5, pp. 2153-2164, 1991.
24. H. T. Laquer, "Asymptotic limits for a two-dimensional recursion," Stud. Appl. Math., vol. 64, p. 271, 1981.
25. Z. Michalewicz, Genetic Algorithms + Data Structures = Evolution Programs. New York: Springer-Verlag, 1992.
26. W. Miller, "Building multiple alignment from pairwise alignments," Comput. Applicat. Biosci., vol. 9, pp. 169-176, 1993.
27. E. W. Myers and W. Miller, "Optimal alignments in linear space," Comput. Applicat. Biosci., vol. 4, no. 1, pp. 11-17, 1988.
28. M. Roytberg, "A search for common patterns in many sequences," Comput. Applicat. Biosci., vol. 8, pp. 57-64, 1992.
29. D. Sankoff, "Matching sequence under deletion-insertion constraints," in Proc. Nat. Acad. Sci. Washington, DC: Academy, 1972, vol. 64, pp. 4-6.
30. D. Sankoff, R. J. Cedergren, and W. McKay, "A strategy for sequence phylogeny research," Nucleic Acids Res., vol. 10, pp. 421-431, 1982.
31. W. M. Spears and K. A. De Jong, "Using genetic algorithms for supervised concept learning," in Proc. Tools Artificial Intelligence. Los Alamitos, CA: IEEE Comput. Soc. Press, 1990, pp. 335-341.
32. 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 Res., vol. 22, no. 22, pp. 4673-4680, 1994.
33. R. Unger and J. Moult, "Genetic algorithms for protein folding simulations," J. Mol. Biol., vol. 231, pp. 75-81, 1993.
34. M. Vingron and P. Argos, "Motif recognition and alignment for many sequences by comparison of dot-matrices," J. Mol. Biol., vol. 218, pp. 33-43, 1991.
35. M. Vihinen, A. Euranto, P. Luostarinen, and O. Nevalainen, "MULTICOMP: A program package for multiple sequence comparison," Comput. Applicat. Biosci., vol. 8, pp. 35-38, 1992.
36. M. S. Waterman, "General methods of sequence comparison," Bull. Math. Biol., vol. 46, pp. 473-500, 1984.
37. _, "Multiple sequence alignment by consensus," Nucleic Acids Res., vol. 14, pp. 9095-9102, 1986.
38. B. P. Buckles, F. E. Petry, and R. L. Kuester, "Schema survival rates and heuristic search in genetic algorithms," in Proc. Tools Artificial Intelligence. Los Alamitos, CA: IEEE Comput. Soc. Press, 1990.