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研究生:曾雲輝
研究生(外文):Yun-Huei Tzeng
論文名稱:估計同義與不同義的鹼基取代速率的方法及其應用
論文名稱(外文):Methods for Estimating Rates of Synonymous and Non-synonymous Nucleotide Substitutions and Its Application
指導教授:許世壁許世壁引用關係
指導教授(外文):Sze-Bi Hsu
學位類別:博士
校院名稱:國立清華大學
系所名稱:數學系
學門:數學及統計學門
學類:數學學類
論文種類:學術論文
論文出版年:2005
畢業學年度:93
語文別:英文
論文頁數:86
中文關鍵詞:substitution ratesynonymousnonsynonymousKaKsLWL85LPB93Receptor-Like KinaseArabidopsis thalianaRice
外文關鍵詞:substitution ratesynonymousnonsynonymousKaKsLWL85LPB93Receptor-Like KinaseArabidopsis thalianaRice
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There are three chapters in this dissertation and I focus on the comparison and modification of methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions. In chapter 1, I describe the background and terminology of evolutionary change in nucleotide sequences. I also introduce the derivations of two methods for estimating the synonymous and nonsynonymous substitution rates (Ks and Ka) -- Li-Wu-Luo (1985), Li (1993) and Pamilo and Bianchi (1993). In chapter 2, I compared three frequently used methods for estimating the synonymous and nonsynonymous substitution rates (Ks and Ka) -- Li-Wu-Luo (1985), Li (1993) and Pamilo and Bianchi (1993), and Goldman and Yang (1994) as in the PAML package. These methods were evaluated and compared for their accuracies and are denoted by LWL85, LPB93, and GY94, respectively. After comparing their performance, I proposed a correction to improve the accuracies of LWL85 and LPB93 and a modification method, denoted by M-LWL85. In chapter 3, I describe the comparative analysis of the receptor-like kinase family in Arabidopsis thaliana and Rice. This is an application of estimating Ka and Ks in the comparison between different species.
There are three chapters in this dissertation and I focus on the comparison and modification of methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions. In chapter 1, I describe the background and terminology of evolutionary change in nucleotide sequences. I also introduce the derivations of two methods for estimating the synonymous and nonsynonymous substitution rates (Ks and Ka) -- Li-Wu-Luo (1985), Li (1993) and Pamilo and Bianchi (1993). In chapter 2, I compared three frequently used methods for estimating the synonymous and nonsynonymous substitution rates (Ks and Ka) -- Li-Wu-Luo (1985), Li (1993) and Pamilo and Bianchi (1993), and Goldman and Yang (1994) as in the PAML package. These methods were evaluated and compared for their accuracies and are denoted by LWL85, LPB93, and GY94, respectively. After comparing their performance, I proposed a correction to improve the accuracies of LWL85 and LPB93 and a modification method, denoted by M-LWL85. In chapter 3, I describe the comparative analysis of the receptor-like kinase family in Arabidopsis thaliana and Rice. This is an application of estimating Ka and Ks in the comparison between different species.
INTRODUCTION....................................1

CHAPTER 1: Estimating the Number of Nucleotide Substitutions Between Sequences.................5
Introduction....................................5
Juke and Cantor’s One-Parameter Model..........5
Kimura’s Two-Parameter Model...................8
Sequence Similarity............................11
Noncoding Sequences............................12
Protein-Coding Sequences.......................14

CHAPTER 2: Comparison of Three Methods for
Estimating Rates of Synonymous and Non-synonymous Nucleotide Substitutions.......................20
Introduction...................................20
Methods........................................21
Results........................................29
Discussion.....................................35
Tables.........................................39
Figure Legends.................................40
Figures........................................42

CHAPTER 3: Comparative Analysis of the Receptor-Like Kinase Family in Arabidopsis thaliana and Rice........45
Introduction...................................45
Results........................................48
Discussion.....................................56
Methods........................................62
Figure Legends.................................66
Figures........................................71

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