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研究生:黃熙淵
研究生(外文):Hsi-Yuan Huang
論文名稱:應用基因演算法設計多聚合酵素鏈鎖反應的引子
論文名稱(外文):Primer Design for Multiplex PCR Using a Genetic Algorithm
指導教授:洪炯宗洪炯宗引用關係黃憲達黃憲達引用關係
指導教授(外文):Jorng-Tzong HorngHsien-Da Huang
學位類別:碩士
校院名稱:國立中央大學
系所名稱:資訊工程研究所
學門:工程學門
學類:電資工程學類
論文種類:學術論文
論文出版年:2004
畢業學年度:92
語文別:英文
論文頁數:40
中文關鍵詞:引子設計基因演算法多聚合酵素鏈鎖反應
外文關鍵詞:genetic algorithmprimer designmultiplex PCR
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多聚合酵素鏈鎖反應為多個引子在同一聚合酵素鏈鎖反應中反應。由於可同時放大多個目標去氧核醣核酸片段,因此可節省實驗的時間與花費。一個成功的反應有賴於引子的設計,但此引子受限於解鏈溫度,嘌呤嘧啶組成比例,長度及與目標序列的互補狀況,因此為一個相當繁雜的任務。設計引子的方法於這幾十年蓬勃發展,但大多數都不支援多聚合酵素鏈鎖反應。系統主要運用遺傳演算法,模擬自然界的演化方式,對既定問題求最佳解。目前的實驗結果顯示,其可很快的找出目標區域的引子,並將其分組,使它們不只是符合引子設計的原則,並可於同一聚合酵素鏈鎖反應中反應。
Multiplex PCR is the term used when more than one pair of primers is used in a polymerase chain reaction. The goal of multiplex PCR is to amplify several segments of target DNA simultaneously and thereby to conserve template DNA, save time, and minimize expense. The success of above-mentioned methods is dependent on primer design. However, this is a tedious task as too many constrains such as melting temperatures, primer length, GC content and complementarity to optimize the PCR product needs to be satisfied. Various kinds of approaches for designing a primer have been proposed in the last few decades, but most of them don’t satisfy the multiplex PCR. The system draws on genetic algorithm which imitates nature’s process of evolution and genetic operations on chromosomes in order to achieve the optimal solutions. Presently experimental results indicate that the proposed algorithm can find some group of primer pairs that not only obey the design properties but also work at same tube.
Chapter 1 Introduction 1
1.1 Background 1
1.2 Motivation 3
1.3 Goal 4
Chapter 2 Related Works 5
2.1 Constraints of PCR 5
2.2 Constraints of multiplex PCR 6
2.2 Literature reviews 6
Chapter 3 Methods 9
3.1 Unique regions searching 9
3.2 Multiplex PCR primer design using a GA 11
3.2.1 Chromosome 11
3.2.2 GA process flow 12
3.2.3 Fitness 15
3.2.4 Crossover 15
3.2.5 Mutation 17
3.3 Result verification 20
3.4 Parameter determination 20
Chapter 4 Results 23
Chapter 5 Case Studies 25
5.1 Case Study I 25
5.2 Case Study II 26
Chapter 6 Discussions and Conclusions 28
6.1 Characteristics of our tool 28
6.2 Limitations and Future Works 28
6.3 Conclusions 29
References 30
1.Griffin, H.G. and A.M. Griffin, PCR technology : current innovations. 1994. 6.
2.Burke, J.F., PCR : essential techniques. 1996.
3.Sambrook, J. and D.W. Russell, Molecular cloning : a laboratory manual. 3 ed. 2001. 8.107.
4.Innis, M.A., D.H. Gelfand, and J.J. Sninsky, PCR applications : protocols for functional genomics. 1999.
5.Davis, L., Genetic algorithms and simulated annealing, in 1. 1987.
6.Elnifro, E.M., et al., Multiplex PCR: Optimization and Application in Diagnostic Virology. Clin. Microbiol. Rev., 2000. 13(4): p. 559-570.
7.Rozen, S. and H. Skaletsky, Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol, 2000. 132: p. 365-86.
8.Jarman, S.N., Amplicon: software for designing PCR primers on aligned DNA sequences. Bioinformatics, 2004: p. bth121.
9.Rose, T.M., et al., Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res, 1998. 26(7): p. 1628-35.
10.Schoske, R., et al., Multiplex PCR design strategy used for the simultaneous amplification of 10 Y chromosome short tandem repeat (STR) loci. Anal Bioanal Chem, 2003. 375(3): p. 333-43.
11.Goldberg, D.E., Genetic Algorithms in Search, Optimization, and Machine Learning. 1989, New York: Addison-Wesley.
12.Setubal, J. and J. Meidanis, Sequence comparison and database search. In Introduction To Computational Molecular Biology. 1997. 47-103.
13.Ramaswamy, S.V., et al., Single Nucleotide Polymorphisms in Genes Associated with Isoniazid Resistance in Mycobacterium tuberculosis. Antimicrob. Agents Chemother., 2003. 47(4): p. 1241-1250.
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