博碩士論文 91522062 詳細資訊




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姓名 許博凱(Bo-Kai HSU)  查詢紙本館藏   畢業系所 資訊工程學系
論文名稱 蛋白質重複序列分析系統
(ProDup: a software to compute structure internal duplications in protein sequences)
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摘要(中) 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。在文獻上指出,許多較長的蛋白質序列可能是由上一代含有許多重覆序列的蛋白質演化而來,同時也發現許多蛋白質中的重覆序列和其功能與結構有關。本研究試著開發一套蛋白質序列的分析工具稱作(ProDup),可以配合一些額外的資訊,像是二級結構來分析蛋白質序列中的重覆序列。根據這工具的分析我們發現許多有趣的結果。並且拿來和其他找尋蛋白質重覆序列的工具做比較。同時我們也利用這個工具來分析Pfam資料庫中的 repeats families。ProDup可以在蛋白質重覆序列的研究上提供一個不同的觀點。
摘要(英) Protein internal duplications are regular arrays of spatial and functional groups. It is useful for structural packing or for protein-protein interactions. Many large proteins have evolved by internal duplications and many protein internal duplications correspond to functional and structural units. In this study, we develop a system that can find protein internal duplications with user constraints called ProDup. We obtain several interesting results from the finder. We also compare our results with those found by other tools. Furthermore, based on Pfam repeats families, we provide the statistics of the data found by ProDup. ProDup provides an alternative viewpoint of protein internal duplications.
關鍵字(中) ★ 蛋白質重複序列
★ 分析系統
關鍵字(英) ★ secondary structure
★ internal duplication
論文目次 Chapter 1 Introduction 1
1.1 Background 1
1.2 Motivation 2
1.3 Goal 3
Chapter 2 Related Works 4
2.1 PAM (Percent/Point Accepted Mutation) 4
2.2 CLUSTAL W 4
2.3 Databases 5
2.4 TRIPS 8
2.5 Radar 9
2.6 REP 10
2.7 PSIPRED 11
Chapter 3 Materials and Methods 12
3.1 Data Sets 12
3.2 Develop Environment 12
3.3 Main Ideals 12
3.4 Methods 13
Chapter 4 Results 31
4.1 Web Interface 31
4.2 Case Study 32
Chapter 5 Discussions and Conclusions 38
References 41
Appendix 43
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2. Kajava, A.V., Review: proteins with repeated sequence--structural prediction and modeling. J Struct Biol, 2001. 134(2-3): p. 132-44.
3. Andrade, M.A., et al., Homology-based method for identification of protein repeats using statistical significance estimates. J Mol Biol, 2000. 298(3): p. 521-37.
4. Andrade, M.A., C. Perez-Iratxeta, and C.P. Ponting, Protein repeats: structures, functions, and evolution. J Struct Biol, 2001. 134(2-3): p. 117-31.
5. Kohl, A., et al., Designed to be stable: crystal structure of a consensus ankyrin repeat protein. Proc Natl Acad Sci U S A, 2003. 100(4): p. 1700-5.
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7. Sedgwick, S.G. and S.J. Smerdon, The ankyrin repeat: a diversity of interactions on a common structural framework. Trends Biochem Sci, 1999. 24(8): p. 311-6.
8. Bateman, A., et al., The Pfam protein families database. Nucleic Acids Res, 2002. 30(1): p. 276-80.
9. Kurtz, S., et al., Computation and visualization of degenerate repeats in complete genomes. Proc Int Conf Intell Syst Mol Biol, 2000. 8: p. 228-38.
10. TIGER, Repeat-finder. [http://www.tigre.org/tdb/rice/repeatinfo-MUMmer.shtml], 1999.
11. Delcher, A.L., et al., Alignment of whole genomes. Nucleic Acids Res, 1999. 27(11): p. 2369-76.
12. Kurtz, S. and C. Schleiermacher, REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics, 1999. 15(5): p. 426-7.
13. Henikoff, S. and J.G. Henikoff, Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A, 1992. 89(22): p. 10915-9.
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15. Tatusov, R.L., et al., The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res, 2000. 28(1): p. 33-6.
16. Tatusov, R.L., et al., The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 2003. 4(1): p. 41.
17. Apweiler, R., et al., InterPro--an integrated documentation resource for protein families, domains and functional sites. Bioinformatics, 2000. 16(12): p. 1145-50.
18. Bateman, A., et al., The Pfam protein families database. Nucleic Acids Res, 2004. 32 Database issue: p. D138-41.
19. Mulder, N.J., et al., The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res, 2003. 31(1): p. 315-8.
20. Attwood, T.K., The PRINTS database: a resource for identification of protein families. Brief Bioinform, 2002. 3(3): p. 252-63.
21. Corpet, F., J. Gouzy, and D. Kahn, The ProDom database of protein domain families. Nucleic Acids Res, 1998. 26(1): p. 323-6.
22. Katti, M.V., et al., Amino acid repeat patterns in protein sequences: their diversity and structural-functional implications. Protein Sci, 2000. 9(6): p. 1203-9.
23. McGuffin, L.J., K. Bryson, and D.T. Jones, The PSIPRED protein structure prediction server. Bioinformatics, 2000. 16(4): p. 404-5.
24. Adebiyi, E.F., T. Jiang, and M. Kaufmann, An efficient algorithm for finding short approximate non-tandem repeats. Bioinformatics, 2001. 17 Suppl 1: p. S5-S12.
指導教授 洪炯宗、黃憲達
(Jorng-Tzong Horng、Hsien-Da Huang)
審核日期 2004-7-13
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