尋找在為排比的核醣核酸的共同二級結構特徵區塊之演算法

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姓名

周泊彥(Bo-Yen Chou) 查詢紙本館藏

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資訊工程學系

論文名稱

尋找在為排比的核醣核酸的共同二級結構特徵區塊之演算法
(An algorithm for finding common secondary structure motifs in unaligned RNA sequences)

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摘要(中)

核醣核酸分子參加許多的生化反應，如催化，核醣核酸編接，轉譯和轉錄的調控，和蛋白質的交互作用。生化的功能和核醣核酸的結構有高度相關。在核醣核酸後修飾作用和調控有相同功能的區域會有保留的結構或序列。雖然現有工具可以發現保留的序列根據序列的同源和排比，然而更重要的是尋找共同二級結構特徵區塊和它們的功能。我們要建構一個工具可以偵測保留的結構於核醣核酸。這個工具包涵三個部份分別是預測核醣核酸二級結構，發現重複的結構和分類重複的結構。首先用mfold來預測核醣核酸結構。接下來用後秩陣列去發現重複的結構。最後重複的結構被分類成特徵區塊根據結構長度。

摘要(英)

RNA molecules involved with a variety of important biological processes such as catalysis, RNA splicing, regulation of transcription, translation, and protein interactions. These biological function is highly related to the structure folding of an RNA molecule. Studies in RNA such as many trans-acting non-coding RNA genes and cis-acting RNA regulatory elements show that similar functional RNA share conserved structure or sequence. Although there are tools in finding conserved sequence base on sequence homology and alignment, fining common secondary structure motif is not available. We aim to build a tool which can detect structure conservation on RNA sequences. The proposed tool contains three parts which are “predict RNA secondary structure”, “find repeat structures” and “cluster repeat structures”. First, our research use mfold to predict RNA structure. Second, our research use suffix array to find repeat structure. Finally, repeat structures are cluster to motifs by length of the structure. Some case studies are shown to demonstrate there exist structure conservation on some RNA sequence families where sequence variation on these families are high.

關鍵字(中)

★ 特徵區塊
★ 二級結構
★ 核醣核酸

關鍵字(英)

★ secondary structure
★ RNA
★ motif

論文目次

Chapter 1 Introduction 1
1.1 Background 1
1.2 Motivation 3
1.3 Goal 4
Chapter 2 Related Works 5
2.1 Prediction RNA secondary structure 5
2.2 TRANSFAC database 7
2.3 UTRdb and UTRsite 7
2.4 Finding common secondary structure motifs 8
Chapter 3 Method 12
3.1 Predict RNA secondary structure 13
3.2 Find repeat structure 14
3.2.1 Translate structure to sequence type 15
3.2.2 Find repeat substrings by building suffix array 16
3.3 Cluster repeat structure 17
3.3.1 Cluster group 18
3.3.2 Ranking of motifs 24
Chapter 4 Results 29
4.1 Case study I: Iron response element (IRE) 29
4.2 Case study II: Potato virus X cis-acting regulatory element 31
4.3 Case study III: tRNA 32
4.4 Compare our method with RNAProfile and GPR 36
Chapter 5 Conclusions 38
References 41

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指導教授

洪炯宗、黃憲達
(Jorng-Tzong Horng、Hsien-Da Huang)

審核日期

2005-7-21

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