PHGA-COFFEE: Aligning multiple sequences by parallel hybrid genetic algorithm

Jisuanji Xuebao/Chinese Journal of Computers

Volumn 29, Issue 5, 2006, Pages 727-733

  Liu, Li Fang ^a   Huo, Hong Wei ^a   Wang, Bao Shu ^a  

^a XIDIAN UNIVERSITY   (China)

Author keywords

Bioinformatics; Dynamic programming; Multiple sequence alignment; Parallel hybrid genetic algorithm

Indexed keywords

COMPUTER SOFTWARE; DESIGN; DYNAMIC PROGRAMMING; MATHEMATICAL OPERATORS; PARALLEL ALGORITHMS;

BIOINFORMATICS; MULTIPLE SEQUENCE ALIGNMENT; PARALLEL HYBRID GENETIC ALGORITHM; SOFTWARE PHGA COFFEE;

GENETIC ALGORITHMS;

EID: 33745959023     PISSN: 02544164     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (15)

1. Atwood T. K. et al. Luo Jin-Chu et al. translate. Introduction to Bioinformatics. Beijing: Peking University Press, 2001 (in Chinese)
2. 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, 1970, 48(3): 443-453
3. Carrillo H., Lipman D. J.. The multiple sequence alignment problem in biology. SIAM Journal on Applied Mathematics, 1988, 48(5): 1073-1082
4. Hogeweg P., Hesper B.. The alignment of sets of sequences and the construction of phylogenetic trees: An integrated method. Journal of Molecular Evolution, 1984, 20(2): 175-186
5. Feng D. F., Doolittle R. F.. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. Journal of Molecular Evolution, 1987, 25(4): 351-360
6. Taylor W. R.. A flexible method to align large numbers of biological sequences. Journal of Molecular Evolution, 1988, 28(1-2): 161-169
7. Thompson J. D., Higgins D. G., Gibson T. J.. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 1994, 22(22): 4673-4680
8. Notredame C., Higgins D. G.. SAGA: Sequence alignment by genetic algorithm. Nucleic Acids Research, 1996, 24(8): 1515-1524
9. Nguyen H. D., Yoshihara I.. Aligning Multiple Protein Sequences by Parallel Hybrid Genetic Algorithm. Tokyo, Japan: Universal Academy Press, 2002, 123-132
10. Thompson J. D., Plewniak F., Poch O.. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Research, 1999, 27(13): 2682-2690
11. Notredame C., Holm L., Higgins D. G.. COFFEE: An objective function for multiple sequence alignment. Bioinformatics, 1998, 14(5): 407-422
12. Eddy S.. Multiple alignment using hidden Markov models. In: Proceedings of the International Conference on Intelligent Systems for Molecular Biology. Cambridge, England: AAAI/MIT Press, 1995, 114-120
13. Wang L., Jiang T.. On the complexity of multiple sequence alignment. Journal of Computational Biology, 1994, 1(4): 337-348
14. Notredame C.. Recent progresses in multiple sequence alignment: A survey. Pharmacogenomics, 2002, 3(1): 131-144
15. Henikoff S., Henikoff J. G.. Amino acid substitution matrices from protein blocks. In: Proceedings of the National Academy of Sciences of the USA, Washington, USA, 1992, 10915-10919