功能性核醣核酸模體之整合性分析系統

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姓名

張資昊(Tzu-Hao Chang) 查詢紙本館藏

畢業系所

資訊工程學系

論文名稱

功能性核醣核酸模體之整合性分析系統
(A Web-based System to Integrate RiboSW, RNALogo, and RNAMST for Comprehensive Analysis of Functional RNA Motifs)

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摘要(中)

核醣核酸分子參與許多生物程序，如基因的調控與蛋白質的合成。研究功能性核醣核酸模體(functional RNA motif)可獲得有用之資訊於瞭解核醣核酸之調控機制。近年來，許多資料庫累積了各種不同類型功能性核醣核酸模體之資料，並有許多計算方法被建立使用於分析核醣核酸序列中之功能性核醣核酸模體。然而，目前仍缺乏一個整合性系統，將這些資料與分析方法整合在一起，以提供使用者一個綜合性分析流程於探索功能性核醣核酸模體。本研究目的即是設計與實作一個整合性網頁介面系統—fRNAfinder，以幫助使用者便利地與廣泛地研究分析核醣核酸序列中之功能性核醣核酸模體。
fRNAfinder提供了三種主要功能：辨識輸入核醣核酸序列中之已知功能性核醣核酸模體之相似物；發現輸入核醣核酸序列中之保留性核醣核酸模體；搜尋使用者描述之核醣核酸模體之相似物於數個核醣核酸序列資料庫。此系統整合了各種相關資料與分析方法，並建立了一個容易使用之網頁介面，讓使用者不需下載安裝，即可方便地使用各種分析程序。此外，本研究開發了三個新穎的方法—RiboSW、RNALogo、RNAMST，以增進此系統分析與呈現之能力。RiboSW能有效地辨識核醣核酸序列中之riboswitches；RNALogo能良好地呈現結構性核醣核酸模體之特性；RNAMST能快速有效地搜尋使用者描述之核醣核酸模體之相似物於數個核醣核酸序列資料庫之中。此系統之預測結果皆以良好的圖形視覺化方式呈現於網頁上。因此，我們認為此系統有助於使用者方便地與廣泛地分析核醣核酸序列中之功能性核醣核酸模體。

摘要(英)

In this Dissertation, we present an integrated web-based system, fRNAfinder, to facilitate user comprehensively analyzing functional RNA motifs against RNA sequences. Though our easy-to-use web server, users can conveniently identify homologs of various known functional RNA motifs in an RNA sequence, discover conserved RNA motifs in related RNA sequences, and search user-specified RNA motif against numerous RNA sequence databases. Various analytical approaches and data sources were incorporated into fRNAfinder. In addition, three novel approaches, RiboSW, RNALogo and RNAMST, were developed and incorporated to enhance ability of fRNAfinder. RiboSW efficiently and conveniently identifies riboswitches within RNA sequences. RNALogo provides a new graphical representation of the pattern in structural RNA motifs. RNAMST efficiently and flexibly searches user-specified RNA motif against RNA databases. The predictive results and related information are presented with good graphical visualization on fRNAfinder web page. fRNAfinder is an integrated web server which facilitates user conveniently and comprehensively analyzing functional RNA motifs against RNA sequences. fRNAfinder is available at http://bioinfo.csie.ncu.edu.tw/fRNAfinder/

關鍵字(中)

★ 核醣核酸
★ 核醣核酸模體
★ 核醣核酸結構

關鍵字(英)

★ RNA
★ functional RNA
★ RNA motif
★ RNA structure

論文目次

摘要 V
Abstract VI
誌謝 VII
Table of Contents VIII
List of Figures X
List of Tables XII
Chapter 1 Introduction 1
1.1 Background 2
1.2 Motivation, Problem Statements, and Research Goal 12
1.3 Related Works 14
1.4 Organization of this Dissertation 24
Chapter 2 Architecture of the Integrated Web-based System 26
Chapter 3 Identification of Homologs of Known Functional RNA Motifs in an RNA Sequence 28
3.1 Introduction 28
3.2 Design and Implementation 32
3.3 Results 41
3.4 Case Study 49
3.5 Summary 52
Chapter 4 Discovery of Conserved RNA Motifs in Related RNA Sequences 53
4.1 Introduction 53
4.2 Design and Implementation 57
4.3 Results 63
4.4 Case Studies 67
4.5 Summary 73
Chapter 5 In Search of User-specified RNA Motif against Numerous RNA Sequence Databases 74
5.1 Introduction 74
5.2 Materials and Methods 75
5.3 Results 78
5.4 Case Study 86
5.5 Summary 87
Chapter 6 In Comparison with Other Works 89
Chapter 7 Conclusions and Future Works 95
Bibliographies 97

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指導教授

洪炯宗(Jorng-Tzong Horng)

審核日期

2009-10-7

推文