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系統識別號 U0026-2306201614225500
論文名稱(中文) 應用轉移矩陣法來檢測次世代基因定序資料之鹼基游移現象
論文名稱(英文) Applying Transition Matrix to Monitor the Shift Movement of Bases for Next Generation Sequencing Data
校院名稱 成功大學
系所名稱(中) 統計學系
系所名稱(英) Department of Statistics
學年度 104
學期 2
出版年 105
研究生(中文) 王昱慈
研究生(英文) Yu-Tzu Wang
學號 R26034056
學位類別 碩士
語文別 英文
論文頁數 35頁
口試委員 指導教授-詹世煌
口試委員-馬瀰嘉
口試委員-孫孝芳
中文關鍵字 次世代基因定序  鹼基品質  轉移矩陣 
英文關鍵字 Next generation sequencing  base quality  transition matrix 
學科別分類
中文摘要 隨著科技的發展,DNA 定序的技術已進步許多。了解DNA 分子的核甘酸排列順序不僅能夠了解全基因組,同時能在醫藥、健康和其他領域有重大的突破。由於分子結構以及定序過程的不確定性,對鹼基定序的品質可能會有很大的影響。文獻已經廣泛探討過鹼基定序的品質,但是對鹼基位移的研究卻相當缺乏。現有研究雖已指出鹼基定序出現的位置並非固定,但對其位移的方向仍未得知。本研究利用轉移矩陣之方法,針對Illumina Miseq 平台的次世代基因定序資料監控鹼基的位移。研究結果顯示本方法確實能偵測週期之間鹼基的位移及位移的方向。
英文摘要 As science develops, the technology of DNA sequencing have progressed tremendously. Understanding the serial order of nucleotides within a DNA molecule will be a great help to realize the whole genome expression, and consequently make important breakthroughs in areas of medicine, health science and others simultaneously. Due to the variation of molecular structure, the accuracy of base calling does raise the issue of in the quality of sequence assembly. While the quality of base calling has been extensively investigated, the shift movement of bases is relatively unexplored. Several researches have been conducted and proved that the positions of bases are not fixed, however, the direction of shift movement has not been studied so far. The purpose of this thesis focuses on monitoring the shift movement of bases for next generation sequencing (NGS) data from Illumina Miseq platform by using transition matrix. The result of this study showed the existence of shifts over cycles, and the shift movement direction could be detected by the transition matrix method.
論文目次 摘要 ii
Abstract iii
Acknowledgements iv
Table of Contents v
List of Tables vi
List of Figures vii
Chapter 1. Introduction 1
Chapter 2. Literature Review 2
2.1 DNA Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2.2 Shift Movement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Chapter 3. Materials and Methods 4
3.1 Data Collection and Data Processing . . . . . . . . . . . . . . . . . . . . . . 4
3.2 Determination of Real Base . . . . . . . . . . . . . . . . . . . . . . . . . . 7
3.2.1 Cluster Positions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
3.2.2 Intensity Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.2.3 Base Calling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
3.3 Transition Matrix, State Vector and Steady-state . . . . . . . . . . . . . . . . 13
Chapter 4. Simulation 15
4.1 Setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
4.2 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Chapter 5. Application of NGS Data 23
5.1 Data Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
5.2 Analysis of Transition Matrix for Adjustment Data . . . . . . . . . . . . . . 24
5.3 Comparison of Shift Pattern for Raw Data and Adjustment Data . . . . . . . 27
Chapter 6. Conclusion 30
References 31
Appendix A. Time Homogeneity Test 33
Appendix B. Long-range Prediction 34
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