Multiple sequence alignment using evolutionary programming

Proceedings of the 1999 Congress on Evolutionary Computation, CEC 1999

Volumn 1, Issue , 1999, Pages 445-452

  Chellapilla, K ^a   Fogel, G B ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b NATURAL SELECTION INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COMPUTER PROGRAMMING; NUCLEIC ACIDS;

COMMON STRUCTURES; EVOLUTIONARY PROGRAMMING ALGORITHMS; MULTIPLE SEQUENCE ALIGNMENT ALGORITHM; MULTIPLE SEQUENCE ALIGNMENTS; VARIATION OPERATOR;

EVOLUTIONARY ALGORITHMS;

EID: 84901397420     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CEC.1999.781958     Document Type: Conference Paper

References (27)

1. Anabarasu, L. A., Narayanasamy, P., and Sundararajan, V. (1998) Multiple sequence alignment using parallel genetic algorithms. In: The Second Asia-Pacific Conference on Simulated Evolution And Learning (SEAL-98), X. Yao, R. McKay, C. S. Newton, J. H. Kim and T. Furuhashi (eds.).
2. Brunk, C. F. and Sadler, L. A. (1990) Characterization of the promoter region of Tetrahymena genes, Nuc. Acids Res. 18(2):323-329.
3. Brunk, C. F., Kahn R. W., and Sadler, L. A. (1990) Phylogenetic relationships among Tetrahymena species determined using the polymerase chain reaction, J. Mol Evol. 30:290-297.
4. Briffeuil, P., Baudoux, G., Lambert, C, DeBolle, X., Vinala, C, Feytmans, E., and Depiereux, E. (1998) Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions, Bioinformatics 14(4):357-366.
5. Chan, S. C., Wong, A. K. C., and Chiu, D. K. Y. (1992) A survey of multiple sequence comparison methods, Bull. Math. Biol. 54(4):563-598.
6. Fields, D. S. and Gutell, R. R. (1996) An analysis of large rRNA sequences folded by a thermodynamic method. Current Biology 1:419-430.
7. Fogel, D. B. (1995) Evolutionary Computation: Towards a New Philosophy of Machine Intelligence, IEEE Press, New York.
8. Godzik, A. and Skolnick, J. (1994) Flexible algorithm for direct multiple alignment of protein structures and sequences. CABIOS 10(6):587-596.
9. Gonzalez, R. R., Izquierdo, CM., and Seijas, J. (1998) Multiple protein sequence comparison by genetic algorithms. In: Proceedings of SPIE: Applications and Science of Computational Intelligence (SPIE-98), S. K. Rogers, D. B. Fogel, J. C. Bezdek, and B. Bosacchi (eds.). pp. 99-102. SPIE-The International Society for Optical Engineering, Bellingham, Washington.
10. Gotoh, O. (1982) An improved algorithm for matching biological sequences, J. Mol. Biol. 162:705-708.
11. Higgins, D. G. and Sharp, P. M. (1988) CLUSTAL: a package for performing multiple sequence alignments on a microcomputer, Gene 73, 237-244.
12. Hori, H. and Osawa, S. (1979) Evolutionary change in 5SRNA secondary structure and a phylogenetic tree of 54 5SRNA species, Proc. Natl. Acad. Sci. USA 76:381:385.
13. Kim, J., Pramanik, S. and Chung, M. J. (1994) Multiple sequence alignment using simulated annealing. CABIOS 10(4):419-426.
14. Myers, E. W. and Miller, W. (1988) Optimal alignments in linear space, CABIOS 4(1):11-17.
15. Needleman, S. B. and Wunsch, CD. (1970) A general method applicable to the search for similarities in the amino acid sequence for two proteins, J. Mol. Biol. 48:443-453.
16. Notredame, C. and Higgins, D. G. (1996) SAGA: sequence alignment by genetic algorithm. Nuc. Acids Res. 24:1515-1524.
17. Notredame, C, O'Brien, E. A., and Higgins, D. G. (1997) RAGA: RNA sequence alignment by genetic algorithm. Nuc. Acids Res. 25:4570-4580.
18. Notredame, C, Holm, L., and Higgins, D. G. (1998) COFFEE: an objective function for multiple sequence alignments. Bioinformatics 14(5):407-422.
19. Rempe, U. (1987) Characterizing DNA variability by stochastic matrices, in Classification and Related Methods of Data Analysis, H. H. Bock (Ed.) Amsterdam: Elsevier.
20. Sankoff, D., Abel, Y., Cedergren, R. J., and Gray, M. W. (1987) Supercomputing for molecular cladistics, in Classification and Related Methods of Data Analysis, H. H. Bock (Ed.). Amsterdam: Elsevier.
21. Sankoff, D. (1972) Matching sequence under deletion-insertion constraints, Proc. Natl. Acad. Sci. USA 64:4-6.
22. Sellers, P. (1974) An algorithm for the distance between two finite sequences. Comb. Theory 16:253-258.
23. Sneath, H. A. and Sokal, R. R. (1973). Numerical Taxonomy. San Francisco: W. H. Freeman.
24. Waterman, M. S., Smith, T. F., and Beyer, W. A. (1976) Some biological sequence metrices. Adv. Math 20:367-387.
25. Wilbur, W. J. and Lipman, D. J. (1983) Rapid similarity searches of nucleic acid and protein data banks. Proc. Natl. Acad. Sci. USA 80:726-730.
26. Wong, A. K. C, Liu, T. S., and Wang, CC. (1976) Statistical analysis of residue variability in cytochrome C, J. Mol. Biol. 102:287-295.
27. Zhang, C. and Wong, A. K. C. (1997) A genetic algorithm for multiple molecular sequence alignment, CABIOS 13(6):565-581.