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| 研究生： |
李大華 Dai Hua, Lee |
|---|---|
| 論文名稱： |
生物資訊引子設計系統之設計與實作 Bioinformatics Web-based Primer Design System: @Primer |
| 指導教授： |
謝明華
蔡瑞煌 |
| 學位類別： |
碩士
Master |
| 系所名稱： |
商學院 - 資訊管理學系 Department of Management Information System |
| 論文出版年： | 2003 |
| 畢業學年度： | 91 |
| 語文別： | 英文 |
| 論文頁數： | 75 |
| 中文關鍵詞： | 生物資訊 、引子設計 、聚合酶連鎖反應 |
| 外文關鍵詞： | Bioinformatics, Primer Design, PCR |
| 相關次數： | 點閱：146 下載：39 |
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由於生物科技的蓬勃發展，加上人類基因體的序列草圖在電腦快速的運算能力配合之下已逐步完成，許多生物科技企業或生物學家，已早早開始投入生物資訊的領域中，而生物科技的領域是廣闊無垠的，只有在電腦的配合下，才能快速且準確的得到所想要的結果。而PCR技術的出現，對整個生物界可說是一埸不小的衝擊與革命。大大減少了以往所需的時間和資源。
有鑒於以上的發展，本研究乃著手收集PCR相關文獻，整理分析相關知識及相關生技公司職員討論後作為研究基礎，本研究從資訊的角度切入，以Microsoft .Net為實作平台，C# 和ASP.Net 程式語言，提供生物學家一個方便使用的跨平台網路介面，並能讓生物學家從任何地方、任何時候來使用。並導入OOA/OOP的系統架構概念，將可以提高系統功能的再使用性與整體架構的擴充性。
在本研究中以PCR(Polymerase Chain Reaction)中的引子設計為主要實作目標。且設計一個簡化版本的Multiplex PCR提供生物學家使用。而主要會影響Primer Design的優劣因素有以下這些：Melting Temperature, Annealing Score, GC content, Primer length,因此本研究使用這些因素來做為本研究選擇Primer的因素，並設計了Primer Design Algorithm來篩選出合適的引子。接著設計Primer Scoring Model用來評量引子的分數，並提供生物學家一個選擇的標準，也加入了權重的觀念，好讓使用者調整適合實驗的參數之重要性。
The invention of PCR (Polymerase Chain Reaction) has revolutionized bioinformatics and molecular technology. PCR can amplify specific region of DNA sequence in few minutes. One of these critical parameters is the selection of short oligonucleotides, which called primer. To design the suitable primers is still not part of any standardized algorithm, and several different sets of rules or criteria have been proposed to control the selection of primer sequence.
Our research results include the followings: we have created a general-purpose application that design for primer design with relative PCR domain knowledge. We have also implemented a prototype system with Microsoft new OOP language, C#. We also provide a simplify version of Multiple PCR, it could handle two DNA templates to produce qualified multiple primer sets. This program can scan entire gene sequences for all possible primer pairs obeying these primer design rules and displays information such as the length and melting temperature of each primer, which may be of additional help in choosing primers. This program allows the stringency of certain criteria to be varied for better suit the requirement of particular experiment. We try to provide a convenient computerized tool which has a friendly user interface for biologists or scientists to use easily. The design of our system is based on OOA (Object-Oriented Analysis) and OOP (Object-Oriented Programming). Therefore programmers can easily change some algorithm or updated biology data to improve the efficiency of our primer design system.
CHAPTER 1 INTRODUCTION 1
1.1 Research Motivation 1
1.2 Research Purpose 2
1.3 Research Process 2
1.4 Chapter Structure 3
CHAPTER 2 CONCEPTS OF BIOINFORMATICS AND PROBLEM DESCRIPTION 4
2.1 Bioinformatics 4
2.2 Polymerase Chain Reaction (PCR) 5
2.2.1 Introduction of PCR 5
2.2.2 Process of PCR 7
2.3 The Problem of PCR 8
2.4 Multiplex PCR 10
CHAPTER 3 PRIMER DESIGN CRITERIA 12
3.1 Melting Temperature 12
3.2 Self-Annealing and Self-end Annealing 14
3.3 Pairs Annealing and Pairs-end Annealing 16
3.4 GC Content 17
3.5 Primer Length 17
3.6 Introduction to Nearest-Neighbor Model 18
3.6.1 Nearest-Neighbor Model to Predict Stability 18
3.6.2 Components of Nearest-Neighbor Model 19
3.6.3 Improved Nearest-Neighbor Model to Predict Stability 19
CHAPTER 4 PRIMER DESIGN SYSTEM MODEL AND DESIGN 23
4.1 Concepts of Primer Design Model 23
4.2 The Algorithm of Primer Design System 24
4.2.1 Primer Design Algorithm 25
4.2.2 Limitation of Primer Design algorithm 26
4.2 Primer Design Scoring Model 27
4.2.1 Single Primer Design Scoring Model 27
4.2.2 Multiplex PCR Primer Design Scoring Model 29
4.3Primer Design System Flow 34
4.3.1 Step1 Flow 35
4.3.2 Step2 Flow 38
4.3.3 Step3 Flow 38
4.4 Multiplex PCR Primer Design System Flow 39
4.4.1 Step1 Flow 40
4.4.2 Step2 Flow 42
4.4.3 Step3 Flow 45
4.5 System Development Environment 46
CHAPTER 5 SYSTEM ANALYSIS AND DEMONSTRATION 48
5.1 System Analysis 48
5.1.1 Use Case Diagram 48
5.1.2 Class Diagram 49
5.1.3 Sequence Diagram 53
5.2 System Demonstration 57
5.3 Limitation of our primer design system 65
CHAPTER 6 CONCLUSION AND SUGGESTIONS 66
6.1 Conclusion 66
6.2 Suggestions and Future Development 67
REFERENCE 68
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