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Articles
  • Optimization with Genetic Algorithm for Outcome of Multiple Sequence Alignments for Proceedings of the International Conference on Bioinformatics and Biomedical Engineering (ICBBE 2014)   [iCBBE 2014]
  • Author(s)
  • Hongbin Li, Meile Zhang
  • ABSTRACT
  • Sequence alignment method refers to the residues column position arrangement of two or more sequences by removing or inserting vacancy in biology sequences file (protein or nucleic acid), which can obtain the correlation information between the sequences. The authors developed a kind of optimization package with genetic algorithm for outcome of MSA, which can initialize with random mode or seed mode, and improve the outcome of MSA with the selected fitness function as COFFEE, SPS or WSPS, and some other GA parameters as cross rate, mutation rate, substitution matrix and terminate condition. These improvements are very important to the subsequent analysis as genotyping, clustering of species, conserved motif discovery or mutation identification.
  • KEYWORDS
  • no keyword
  • References
  • [1]
    D. E. Goldberg, 1989, "Genetic algorithms in search, optimization, and machine learning", Reading Menlo Park: Addison-wesley.
    [2]
    Notredame C., D. G. Higgins, 1996, "SAGA: sequence alignment by genetic algorithm", Nucleic acids research, 24(8): 1515-1524.
    [3]
    Durbin R., S. R. Eddy, Krogh A., et a, 1998, "Biological sequence analysis: probabilistic models of proteins and nucleic acids", Cambridge university press.
    [4]
    M. O. Dayhoff, R. M. Schwartz, 1978, " A model of evolutionary change in proteins", In atlas of protein sequence and structure.
    [5]
    Henikoff S, J. G. Henikoff, 1992, "Amino acid substitution matrices from protein blocks[J]. Proceedings of the national academy of sciences", 89(22): 10915-10919.
    [6]
    S. F. Altschul, 1989, "Gap costs for multiple sequence alignment", Journal of theoretical biology, 138(3): 297-309.
    [7]
    S. F. Altschul, 1989, R. J. Carroll, D. J. Lipman, 1989, "Weights for data related by a tree", Journal of molecular biology, 207(4): 647-653.
    [8]
    Notredame C, Holm L, D. G. Higgins, 1998, "COFFEE: an objective function for multiple sequence alignments", Bioinformatics, 14(5): 407-422.
    [9]
    J. D. Thompson, Plewniak F, Poch O, 1999, "BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs", Bioinformatics, 15(1): 87-88.
    [10]
    Thomsen R, G. B. Fogel, Krink T, 2002, "A clustal alignment improver using evolutionary algorithms", Evolutionary computation, CEC'02. Proceedings of the 2002 congress on. IEEE, 1: 121-126.
    [11]
    Liu L, Huo H, Wang B,2005, "HGA-COFFEE: aligning multiple sequences by hybrid genetic algorithm", Advanced data mining and applications, Springer Berlin Heidelberg, 464-473.
    [12]
    Katoh K, Misawa K, Kuma K, et al, 2002, "MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform", Nucleic acids research, 30(14): 3059-3066.

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