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研究生: 林靜媚
Ching-mei Lin
論文名稱: 使用遺傳演算法解多序列排比的問題
Using Genetic Algorithms to Solve Multiple Sequence Alignments
指導教授: 洪炯宗
Jorng-Tzong Horng
口試委員:
學位類別: 碩士
Master
系所名稱: 資訊電機學院 - 資訊工程學系
Department of Computer Science & Information Engineering
畢業學年度: 88
語文別: 中文
論文頁數: 41
中文關鍵詞: 分子序列分析遺傳演數法多序列排比
外文關鍵詞: molecular sequence analysis, genetic algorithm, multiple sequence alignment
相關次數: 點閱:11下載:0
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  • 多序列排比是分子序列分析上一個重要的工具。在演化的過程中,分子序列可能會發生許多的突變,例如插入、刪除、替代等突變事件; 而這些突變造成分子列序間的各種差異。多序列排比是透過同時比較多個序列,以找出序列之間的相似區域,故可找出序列間的結構關係。
    本論文提出一個遺傳演算法,來解決多序列排比的問題。我們使用十七個序列的資料集合來測試我們所提出的方法,並且將我們的實驗結果與其它方法做比較。我們發現我們的方法在大多數具有高相似性的測試資料中擁有不錯的表現。


    Multiple sequence alignment is an important tool in molecular
    sequence analysis. In the evolutionary process, molecular sequences may have several mutations, such as insertion, deletion and substitution. These mutation events result in the diversified difference between sequences. Multiple sequences alignment can help compare the structure-relationship between sequences by simultaneously aligning multiple sequences to find the similar regions.
    This thesis presents genetic algorithms to solve multiple sequence alignments. Several data sets are tested and the experimental results are compared with other methods. We find our approach could obtain good performance in the majority of data sets with high similarity and long sequences.

    1. Introduction 1.1 Motivation 1.2 Problem Description 1.3 Organization of The Thesis 2. Related Work 2.1 Optimal alignment of Two Sequences 2.2 The Sum-of-Pairs Measure For Multiple Sequences Alignment 2.3 Literature of Multiple Sequence Alignment 3. Method 3.1 Chromosomes 3.2 System Process Flow 3.3 Fitness 3.4 Crossover 3.5 Mutation 4. Experiments And Results 4.1 Environment of Implementation 4.2 Experiments 5. Conclusion Bibliography Appendix Data Set

    [AvL87]E.H.L. Aart and P.J.M. van Laarhoven.
    Simulated Annealing: a Review of Theory and Applications.
    Kluwer Academic, Amsterdam, 1987.
    [CF99]Kumar Chellapilla and Gary B. Fogel.
    Multiple sequence alignment using evolutionary programming.
    Congress on Evolutionary Computation, pages 445-452, 1999.
    [CWC92]S. C. Chan, A. K. C. Wong, and D. K. Y. Chiu.
    A survey of multiple sequence comparison methods.
    Bulletin of Mathematical Biology, 54:563-598, 1992.
    [FD87]Da-Fei Feng and Russell F. Doolittle.
    Progressive sequence alignment as a prerequisite to correct phylogenetic trees.
    Journal of Molecular Evolution, 25:351-360, 1987.
    [Gol89]D. E. Goldberg.
    Genetic Algorithms in Search, Optimization, and Machine Learning.
    Addison-Wesley, New York, 1989.
    [Got89] O. Gotoh.
    An improved algorithm for matching biological sequences.
    Journal of Molecular Biology, 162:705-708, 1989.
    [HS88]D.G. Higgins and P.M. Sharp.
    CLUSTAL: a package for performing multiple sequence alignments on a microcomputer.
    Gene, 73:237-244, 1988.
    [IWS96]M. Isokawa, M. Wayama, and T. Shimizu.
    Multiple sequence alignment using a genetic algorithm.
    Genome Informatics, 7:176-177, 1996.
    [Jon88]K. De Jong.
    Learning with genetic algorithms: An overview.
    In Machine Learning 3, pages 121-138. Kluwer, Hingham, MA, 1988.
    [JWD80]R. A. Jue, N. W. Woodbury, and R. F. Doolittle.
    Sequence homologies among e. coli ribosomal proteins: evidence for evolutionary related groupings and internal duplications.
    Journal of Molecular Evolution, 15:129-148, 1980.
    [LAB+93]C.E. Lawrence, S.F. Altschul, M.S. Boguski, J.S. Liu, A.F. Neuwald, and J.C. Wootton.
    Detecting subtle sequence signals: a gibbs sampling strategy for multiple alignment.
    Science, pages 208-214, 1993.
    [MM88]E. W. Myers and W. Miller.
    Multiple sequence alignment using simulated annealing.
    Computer Applications in the Biosciences, 4(1):11-17, 1988.
    [Mor99]B. Morgenstern.
    DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
    Bioinformatics, 15:211-218, 1999.
    [MRS85]M. Murata, J. S. Richardson, and J. L. Sussman.
    Simultaneous comparison of three protein sequences.
    In Proceedings of the National Academy of Science U. S. A., volume 82, pages 3073-3077, 1985.
    [NH96]Cedric Notredame and Desmond G. Higgins.
    SAGA: sequence alignment by genetic algorithm.
    Nucleic Acids Research, 24(8):1515-1524, 1996.
    [NOH97]Cedric Notredame, Emmet A. O''Brien, and Desmond G. Higgins.
    Raga: Rna sequence alignment by genetic algorithm.
    Nucleic Acids Research, 25(22):4570-4580, 1997.
    [NW70]S. B. Needleman and C. D. Wunsch.
    A general method applicable to the search for similarities in the amino acid sequences of two proteins.
    Journal of Molecular Biology, 42:245-161, 1970.
    [PW96]Sankar K. Pal and Paul P. Wang.
    Genetic algorithms for pattern recognition.
    CRC Press, Boca Raton, 1996.
    [San72]D. Sankoff.
    Matching sequence under deletion-insertion constraints.
    In Proceedings of the National Academy of Science U. S. A., volume 64, pages 4-6, Washington, DC, 1972. Academy.
    [SM97]Joao Setubal and Joao Meidanis.
    Sequence comparison and database search.
    In Introduction To Computational Molecular Biology, pages 47-103. PWS, 1997.
    [Sto98]Jens Stoye.
    Multiple sequence alignment with the divide-and-conquer method.
    Gene, 211(2):GC45-GC56, 1998.
    [THG94]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, 22(22):4673-4680, 1994.
    [Wat84]M. S. Waterman.
    General methods of sequence comparison.
    Bulletin of Mathematical Biology, 46:473-500, 1984.
    [Whi94]Darrell Whitley.
    A genetic algorithm tutorial.
    Statistics and Computing, 4:65-85, 1994.
    [WJ94]L. Wang and T. Jiang.
    On the complexity of multiple sequence alignment.
    Journal of Computational Bioloby, 1(4):337-348, 1994.
    [WTS95]M. Wayama, K. Takahashi, and T. Shimizu.
    An approach to amino acid sequence alignment using a genetic algorithm.
    Genome Informatics, 6:122-123, 1995.
    [ZW97a]Ching Zhang and Andrew K. C. Wong.
    A genetic algorithm for multiple molecular sequence alignment.
    Computer Applications in the Biosciences, 13(6):565-581, 1997.
    [ZW97b]Ching Zhang and Andrew K. C. Wong.
    Toward efficient multiple molecular sequence alignment: A system of genetic algorithm and dynamic programming.
    IEEE Transactions on Systems, Man, and Cybernetics-part B: Cybernetics, 27(6):918-932, 1997.

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