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研究生:杜睿評
研究生(外文):Ray-ping Duh
論文名稱:建構馬可夫模型預測人類表現序列標幟及基因體中微衛星滑動率及最適分佈模型
論文名稱(外文):A Modified Markov Model to Predict Microsatellite Slippage Rate in the Human EST and Genome
指導教授:蔣鎮宇蔣鎮宇引用關係
指導教授(外文):Tzen-yuh Chiang
學位類別:碩士
校院名稱:國立成功大學
系所名稱:生命科學系碩博士班
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2009
畢業學年度:97
語文別:英文
論文頁數:301
中文關鍵詞:微衛星滑動率最適模型檢定馬可夫模型
外文關鍵詞:Markov modelModel fittingMicrosatelliteSlippage rate
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微衛星通常以二至六個鹼基為重複單位分佈於基因體中,已有研究證實有些微衛星會和基因的表現有關聯,所以微衛星的演化過程也被生物學家所重視。它的高密度分佈被認為非單純點突變所造成,一般咸信的主要影響因子為滑動突變。滑動突變會造成微衛星序列呈單位的減少或增加,被認為是造成微衛星長度的主要因子。本篇論文建構了一個新的馬可夫模型,不針對滑動突變作任何實驗前的假設,設法由更大範圍地考慮點突變造成的影響,增加了一個新的因子-前微衛星。在我們的研究中可得到:滑動突變的影響在考慮新的因子之後下降為原本的二十個至四十個百分比,但是仍然為影響微衛星演化的重要因子。本研究也針對滑動率分佈做了模型選擇,發現 S 模型係最適合預測滑動率的模型。這個結果也許可以作預測近緣物種微衛星演化的參考依據。
Some microsatellites have been reported to be associated with genes, hence the evolutionary process of those microsatellites is an interesting topic for researchers. The slippage rate has been noted to be a main factor influencing microsatellite’s evolution. In this study, the slippage rate and slippage rate distribution were taken into consideration. A mathematical model called Markov model and a modified model to an impartial one were employed and no any prior assumption of slippage rate associated with microsatellite length should be made. Besides, a new factor called pre-microsatellite which took mutation effect of out-sequence into consideration was introduced. The results indicate that microsatellite slippage rate influence is diminished from twenty percents to forty percents of origin. However, slippage is still an important factor of microsatellite’s evolution. It is revealed that the slippage distribution fits the S model, so that this model can be used to investigate the evolutionary process in closed relatives. Extraordinary points of data which might be associated with gene are also reported.
Abstract (in Chinese)……………………………………………… i
Abstract (in English)……………………………………………… iii
Acknowledgements (in Chinese)………………………………… v
Contents….…………………………………………………………… vi
List of Tables……………………………………………………… viii
Figures Caption…………………………………………………… ix

Chapter 1: Introduction…………………………………………… 1
Chapter 2: Theory…………………………………………………… 7
Chapter 3: Materials, Methods and Softwares…………………… 13
3.1 Materrials………………………………………………………… 13
3.2 Methods…………………………………………………………… 15
3.3 Softwares………………………………………………………… 18
Chapter 4: Results…………………………………………………… 21
4.1 Abundance………………………………………………………… 22
4.2 Slippage rate distribution shape…………………………… 23
4.3 Model fitting…………………………………………………… 35
Chapter 5: Discussion………………………………………………… 45
Chapter 6: Conclusion……………………………………………… 49
References……………………………………………………………… 51
Appendices: Tables and Figures of Simulation Results
Appendix 1. Microsatellite abundance and slippage…………… 65
Appendix 2. Figures of slippage rate per motif……………… 187
Appendix 3. Model fitting results………………………………… 239
Appendix 4. Extraordinary points report………………………… 295
Vita………………………………………………………………………… 301
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