應用遺傳演算法解序列組合問題

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游昌翰(Chang-Hang Yo) 查詢紙本館藏

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資訊工程學系

論文名稱

應用遺傳演算法解序列組合問題
(Using Genetic Algorithms to Solve Fragment Assembly)

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摘要(中)

序列組合問題在人類基因計畫中的ＤＮＡ定序方面，扮演一個很重要的角色。在本論文裡，我們應用遺傳演算法來解序列組合問題。在研究的過程中，我們根據問題的特性來設計染色體的表示方式、演化和突變的運算子來解序列組合問題。最後我們也將我們的方法和其他相關的方法作一比較。

摘要(英)

Fragment assembly plays an important role in DNA sequences of Human Genome Project. In this thesis, we apply genetic algorithms to solve fragment assembly. The proposed approach is based on the problem’s characteristics to design crossover and mutation operators. We also compare our approach with other works in the literature.

關鍵字(中)

★ 遺傳演算法
★ 序列組合

關鍵字(英)

★ fragment assembly
★ genetic algorithm

論文目次

Chapter 1Introduction1
1.1Motivation2
1.2Problem Description3
1.3Organization of The Thesis3
Chapter 2Related Work4
2.1Definition of Fragment Assembly4
2.2Related Work8
Chapter 3Our Approach13
3.1The Description of Our Approach13
3.2Our Approach15
3.2.1 The Flow of Our Approach16
3.2.2 Chromosome Representation17
3.2.3 Fitness function17
3.2.4 Crossover18
3.2.5 Mutation22
Chapter 4Experiments and Results27
4.1Implementation Environments27
4.2Data Set27
4.3Results29
Chapter 5Conclusion32
Chapter 6References33

參考文獻

Chapter 6 References
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[2]Eagle M.L. and Burks C. (1993) Artificial Generated Data Sets for Testing DNA Sequence Assembly Algorithms Genomics 16:186-288
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[6]Huang, X. (1996). An Improved Sequence Assembly Program. Genomics 33:21-31
[7]Huang, X and Madan, A (1999) CAP3: A DNA Sequence Assembly Problem. Genome Research 9:868-877
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[10] Lin,X., et al.,(1999) Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana Nature 402 (6763), 761-768
[11]Matsumoto, K.I., Arai M., Ishihara, N., Ando, A., Inoko, H., and Ikemura, T. (1992) Cluster of fibronectin type-III repeats found in the human major histocompatibility complex class III region shows highest homology with repeats in tenascin. Genomics 12: 485-491
[12]Needleman, S. B. and Wunsch, C. D. (1970) Ageneral method cpplicable to the search for similarities in the amino acid sequences of two proteins. Journal of Molecular Biology. 42: 161-245
[13]Pal, Sankar K. ,Wang,Paul P. (1996). Genetic algorithm for pattern recognition. Boca Raton: CRC Press.
[14]Parsons, R. J., Forrest, S. and Burks, C. (1995). Genetic Algorithms, operators, and DNA Fragment Assembly. Machine Learning 21 (1-2): 11-33 (1995)
[15]Sanger, F, ;Coulson, A,;Hill,D.; and Petersen,G. 1982 Nucleotide sequence of bacteriophage lambda DNA. J. MOL. Biol.162:729-773
[16]Setubal, J. and Meidanis, J. (1997). Introduction to Computational Molecular Biology, PWS publishing Company
[17] Sverdlov, E. D et al., (1987) Family of human Na+, K+-ATPase genes. Structure of the gene of isoform alpha-III. Dokl. Biochem. 297, 426-431
[18]Tao, G. and Michalewicz, Z. Inver-over Operator for the TSP, Proceedings of the 5th Parallel Problem Solving from Nature, T. Baeck, A.E. Eiben, M. Schoenauer, and H.-P. Schwefel (Editors), Amsterdam, September 27-30, 1998, Springer-Verlag, Lecture Notes in Computer Science, pp.803-812.
[19]Whitely, Darrell (1994). A Genetic Algorithm Tutorial. Statistics and Computing. 4:65-85.

指導教授

洪炯宗(Jorng-Tzong Horng)

審核日期

2000-7-7

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