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研究生： 鄧仕祥
Shr-Shiang Deng
論文名稱： 蛋白質重複序列分析工具
Protein Repeats Finder
指導教授： 洪炯宗
Jorng-Tzong Horng
口試委員:
學位類別： 碩士
Master
系所名稱： 資訊電機學院 - 資訊工程學系
Department of Computer Science & Information Engineering
畢業學年度： 91
語文別： 英文
論文頁數： 58
中文關鍵詞： 蛋白質 、重複序列
外文關鍵詞： repeats, protein
相關次數： 點閱：10  下載：0 
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    • 了解蛋白質的重複序列對於分析蛋白質的空間，功能，結構，以及其彼此間的相互作用是有助益的。本研究試著開發一套蛋白質序列的分析工具，這套工具不僅能找出連續性重複序列及週期性重複的胺基酸,並且最主要的是這套工具可以對分散於蛋白質序列上的相近重複序列做分析。本研究開發之蛋白質重複序列分析工具，簡稱PRF，用來做蛋白質序列分析的工具，使用者可在網頁上直接來使用，同時我們分析SWISS-PROT的12萬條蛋白質序列並將其建成資料庫，進而提供使用者可以藉由網路線上查詢到所需要的資訊。有關PRF的詳情資訊，請參考 URL: http://140.115.155.94.

    Protein repeated sequence patterns may be a mechanism which provides regular arrays of spatial and functional groups, useful for structural packing or for one to one interactions with target molecules, and many large proteins have evolved by internal duplication and many internal sequence repeats correspond to functional and structural units.
    In this study, we purpose to develop a protein repeat analysis tool that can find kinds of protein repeats such as tandem repeats, periodically conserved single amino acid repeats, and approximate repeats. We also provide a variety of statistics the repeats we found. Protein Repeats Finder (PRF) is developed to find kinds of protein repeats in a given protein sequence. Users can use this tool on line to query protein repeats they need. The web site is now available at URL: http://140.115.155.94.

    Contents Chapter 1 Introduction 1 1.1 Motivation 1 1.2 Goal 2 Chapter 2 Related Work 4 2.1 PAM (Percent/Point Accepted Mutation) 4 2.2 Swiss-Prot 4 2.3 CLUSTAL W 4 2.4 Suffix Array 5 2.5 TRIPS 5 2.6 Radar 5 2.7 Dotlet 6 Chapter 3 Materials and Methods 7 3.1 Data Sets 7 3.2 Develop Environment 7 3.3 Main Ideals 7 3.4 Approach 8 (i) Exact repeats 8 (ii) Maximal repeat 8 (iii) Seeds 9 (iv) L-extend 10 (v) R-extend 10 (vi) LR-extend 11 (vii) Relation Matrix 11 3.5 Algorithm 15 3.6 Database Schema 24 Chapter 4 Results 29 4.1 Statistics of Different Protein Repeats 29 A. Protein Length Distribution 29 B. Approximate Repeats Distribution 31 C. Approximate Repeats Length Distribution 32 D. Ratio of (Repeats/Protein Length) 33 E. Ratio of (Length of Repeats/Protein Length) 34 4.2 A Database of Repeatitive Elements in Proteins 36 4.3 Query Interface 41 Chapter 5 Discussion 44 5.1 Relations of Structure 44 5.2 A Comparison of Different Tools 54 5.3 Summary 56 5.4 Future Work 56 References 57

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