應用資料探採於核糖體核糖核酸二級結構之分析

以作者查詢圖書館館藏

、以作者查詢臺灣博碩士

、以作者查詢全國書目

、勘誤回報

、線上人數：37

、訪客IP：3.144.123.24

姓名

方淑芬(Shu-Fen Fang ) 查詢紙本館藏

畢業系所

資訊工程研究所

論文名稱

應用資料探採於核糖體核糖核酸二級結構之分析
(Mining Common Structural Motifs in SSU 16 S Ribosomal RNA Secondary Structures)

相關論文

★ 應用嵌入式系統於呼吸肌肉群訓練儀之系統開發	★ 勃起障礙與缺血性心臟病的雙向研究: 以台灣全人口基礎的世代研究
★ 基質輔助雷射脫附飛行時間式串聯質譜儀微生物抗藥性資料視覺化工具	★ 使用穿戴式裝置分析心律變異及偵測心律不整之應用程式
★ 建立一個自動化分析系統用來分析任何兩種疾病之間的關聯性透過世代研究設計以及使用承保抽樣歸人檔	★ 青光眼病患併發糖尿病,使用Metformin及Sulfonylurea治療得到中風之風險:以台灣人口為基礎的觀察性研究
★ 利用組成識別和序列及空間特性構成之預測系統來針對蛋白質交互作用上的特殊區段點位進行分析及預測辨識	★ 新聞語意特徵擷取流程設計與股價變化關聯性分析
★ 藥物與疾病關聯性自動化分析平台設計與實作	★ 建立財務報告自動分析系統進行股價預測
★ 建立一個分析疾病與癌症關聯性的自動化系統	★ 基於慣性感測器虛擬鍵盤之設計與實作
★ 一個醫療照護監測系統之實作	★ 應用手機開發手握球握力及相關資料之量測
★ 利用關聯分析全面性的搜索癌症關聯疾病	★ 全面性尋找類風濕性關節炎之關聯疾病

檔案

[Endnote RIS 格式]

[Bibtex 格式]

[相關文章]

[文章引用]

[完整記錄]

[館藏目錄]

[檢視]

[下載]

本電子論文使用權限為同意立即開放。
已達開放權限電子全文僅授權使用者為學術研究之目的，進行個人非營利性質之檢索、閱讀、列印。
請遵守中華民國著作權法之相關規定，切勿任意重製、散佈、改作、轉貼、播送，以免觸法。

摘要(中)

核糖體核糖核酸是參與蛋白質合成的重要角色,而其穩定時所呈現的二次結構更是影響功能的重要因素；長度為4的U字型環狀結構,發現古細菌及真細菌在特定位置上會出現序列不同的U字型環狀結構,由於二級結構上的序列多而複雜,本文應用資料探採(Data Mining)技術於核糖體小次單元核糖核酸的二級結構之環狀結構的組合,從探採所得到的序列型樣中,可明顯看出不同物種間存在數個相似結構的組合,這些結構的組合可以幫助生物學家進行其他有關核糖體功能的研究。將得到的相似結構序列應用於決策樹(Decision Tree Induction)的分類技術,從結果得知,相似的結構序列確實是物種分類時的重要資訊。從我們進行的實驗中,包含分類及建演化樹的結果,得知這個研究是可行且富有價值的。

摘要(英)

Some structural motifs, like tetra-loops, in ribosomal RNA are known to functionally implicate in virtually every aspect of protein synthesis. Our aim in this study is to discover common structural motifs (CSMs), which possibly are related to specific domain or functions, within the secondary structures of ribosomal RNAs. After applying data mining techniques to mine the common structural motifs, a machine learning approach is used to find significant discriminating common structural motifs from groups of organisms. By applying to several data sets constructed in this study, it suggests that the CSMs can provide effective information to classify organisms and help biologists understand the functions of ribosomal RNA. From the experiments of the classification of organisms and the construction of phylogenetic trees by CSMs mined, we find our approach is promising.

關鍵字(中)

★ 二級結構
★ 核糖體
★ 資料探勘

關鍵字(英)

★ common motifs
★ data mining
★ rRNA
★ secondary structures

論文目次

Contents
Chapter 1 Introduction1
1.1 Problem Definition4
1.2 Brief Description of Our Method and Goal5
1.3 Organization of the Thesis5
Chapter 2 Related Work6
2.1 Ribosomal RNA Secondary Structures6
2.1.1 Prediction of RNA Secondary Structure8
2.1.2 Databases of Ribosomal RNA Secondary Structures8
2.2 Ribosomal RNA Structural Motifs9
2.2.1 Functional Sites9
2.2.2 Comparative Analysis10
2.2.3 Loop Sequence Analysis in Ribosomal RNA11
2.3 Phylogenetic Analysis Based on Ribosomal RNA Sequences12
2.3.1 Approaches for Reconstructing Phylogenetic Trees13
2.3.2 Structure Impact17
2.4 Data Mining17
2.4.1 Mining Sequential Patterns18
2.4.2 Decision Tree Induction22
Chapter 3 The Process of Our Approach24
3.1 Materials25
3.2 Approach26
3.2.1 Mining Common Structural Motifs26
3.2.2 Constructing Character Matrix27
3.2.3 CSMs Reduction and Classification by Decision Tree Induction28
3.2.4 Reconstructing Phylogenetic Tree Based on CSMs30
3.2.5 Implement of our apporch31
Chapter 4 Experiments and Results32
Chapter 5 Discussions and Summary43
References44
Appendix A48
Data Set48
Appendix B51
Statistics in primary sequences and secondary structures51
Appendix C55
Observation of loop and helix sequences55
Appendix D59
Investigate the frequencies of CSMs for each group of organisms59

參考文獻

References
1.A. K. Jain and R. C. Dubes, “Algorithms for clustering data,” Prentice Hall, (1988).
2.A. Phillips, D. Janies and W. Wheeler. “Multiple sequence alignment in phylogenetic analysis,” Molecular Phylogenetic and Evolution 16, 317-330 (2000).
3.A. Rzhetsky, “Estimating substitution rates in ribosomal RNA genes,” Genetics 141, 771-783 (1995).
4.A. S. Mankin, “Pactamycin resistance mutations in functional sites of 16 S rRNA,” J. Mol. Biol. 274, 8-15 (1997).
5.A. Zharkikh, “Estimation of evolutionary distances between nucleotide sequences,” J. Mol. Evol. 39, 315-29 (1994).
6.B. Efron, E. Halloran and S. Holmes, “Bootstrap confidence levels for phylogenetic trees,” Proc Natl Acad Sci USA 93,13429-13434 (1996).
7.B. Efron, E. Halloran, S. Holmes, “Bootstrap confidence levels for phylogenetic trees,” Proc Natl Acad Sci USA 93, 13429-13434 (1996).
8.B. L. Maidak, J. R. Cole, T. G. Lilburn, C. T. Parker, Jr, P. R. Saxman, R. J. Farris, G. M. Garrity, G. J. Olsen, T. M. Schmidt and J. M. Tiedje, “The RDP-II (Ribosomal Database Project),” Nucl. Acids. Res. 29, 173-174 (2001).
9.C. Merryman, D. Moazed, J. McWhirter and H.F. Noller, “Nucleotides in 16 S rRNA protected by the association of 30 S and 50 S ribosomal subunits,” J. Mol. Biol. 285, 97-105 (1999).
10.C. R. Woese and N. R. Pace, “Probing RNA structure, function and history by comparative analysis,” In The RNA World (Gesteland, R. F. and Atkins, J. F., eds), Cold Spring Harbor, NY (1993).
11.C. R. Woese, O. Kandler and M. L. Wheelis, “Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya,” Proc. Natl. Acad. Sci. USA 87, 4576-4579 (1990).
12.C. R. Woese, S. Winker and R. R. Gutell, “Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops",” Proc. Natl. Acad. Sci. USA, 87, 8467-8471 (1990).
13.C. Tuerk, P. Gauss, C. Thermes, D. R. Groebe, M. Gayle, N. Guild, G. Stormo, Y. D’Aubenton-Carafa, O. C. Uhlenbeck, I. Tinoco, E. N. Jr, Brody and L. Gold, “CUUCGG hairpins: extraordinarily stable RNA secondary structure associated with various biochemical processes,” Proc. Natl Acak. Sci. USA 85, 1364-1368 (1988).
14.D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, B. A. Rapp and D. L. Wheeler, “GenBank,” Nucleic Acids Res. 28, 15-8 (2000).
15.D. J. Williams and K. B. Hall, “Experimental and computational studies of the G[UUCG]C RNA tetraloop,” J. Mol. Biol. 297, 1045-1061 (2000).
16.D. L. Swofford, G. J. Olsen, P. J. Wadell and D. M. Hillis, In Molecular systematics, eds. D. M. Hillis, C. Moritz and B. K. Mable, Sinauer Associates, Sunderland, Massachusetts, pp. 407-514 (1996).
17.E. A. Feigenbaum, P. McCorduck and H. P. Nii, The Rise of the Expert Company, New York: Times Books, 1988.
18.F. Tajima and M. Nei, “Estimation of evolutionary distance between nucleotide sequences,” Mol. Biol. Evol. 1, 269-285 (1984).
19.G. J. Olsen, “Earliest phylogenetic branchings: comparing rRNA based evolutionary trees inferred with various techniques,” Cold Spring Harbor Symp. Quant. Biol. LII, 825-837 (1987).
20.G. Jan, L. S. Shawn and D. S. Gary, “Discovering common stem-loop motifs is unaligned RNA sequences,” Nucleic Acids Res. 29, 2135-2144 (2001).
21.G. Stoesser, W. Baker, A. van den Broek, E. Camon, M. Garcia-Pastor, C. Kanz, T. Kulikova, V. Lombard, R. Lopez, H. Parkinson, N. Redaschi, P. Sterk, P. Stoehr, and M. A. Tuli, “The EMBL nucleotide sequence database,” Nucl. Acids. Res. 29, 17-21 (2001).
22.H. A. Raue, W. Musters, C. A. Rutgers, J. van’t Riet and R. J. Planta, In W. E. Hill, A. Daglberg, R. A. Garrett, P. B. Moore, D. Schlesinger and J. R. Warner (eds), The Ribosome, Structure, Function and Evolution. American Society of Microbiology, Washington, DC. 217-235 (1990).
23.H. F. Noller, D. Moazed, S. Stern, T. Powers, P. N. Allen, J. M. Robertson, B. Weiser and K. Triman, In W. E. Hill, A. Daglberg, R. A. Garrett, P. B. Moore, D. Schlesinger and J. R. Warner (eds), The Ribosome, Structure, Function and Evolution. American Society of Microbiology, Washington, DC. 73-92 (1990).
24.H. F. Liu, Phylogenetic Analysis Workshop, March 5-6, 2001, Taipei. Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan.
25.J. Egebjerg, N. Larsen and R. A. Garrett, In W. E. Hill, A. Daglberg, R. A. Garrett, P. B. Moore, D. Schlesinger and J. R. Warner (eds), The Ribosome, Structure, Function and Evolution. American Society of Microbiology, Washington, DC. 168-179 (1990).
26.J. Felsenstein, “Confidence limits on phylogenies: an approach using the bootstrap,” Evolution 39, 783-791 (1985).
27.J. Felsenstein. Phylogenetic Inference Package (PHYLIP), Version 3.57. Department of Genetics, University of Washington, Seattle, WA. (1995).
28.J. Gorodkin, L. J. Heyer and G. D. Stormo, “Finding the most significant common sequence and structure motifs in a set of RNA sequences,” Nucleic Acids Res. 25, 3724-3732 (1997).
29.J. Gorodkin, S. L. Stricklin and G. D. Stormo, “Discovering common stem-loop motifs in unaligned RNA sequences”, Nucleic Acids Res. 29, 2135-3144 (2001).
30.J. Han and M. Kamber, Data Mining: Concepts and Techniques, Morgan Kaufmann Publishers.
31.J. L. Thorne, N. Goldman and D. T. Jones, “Combining protein evolution and secondary structure,” Mol. Biol. Evol. 13, 666-673 (1996).
32.J. R. Fresco, B. M. Alberts and P. Doty, “Some molecular details of secondary structure of ribonucleicacid,” Nature 188, 98-101 (1960).
33.J. R. Quinlan, “C4.5 Programs for machine learning,” Morgan Kaufmann Publishers, San Mateo, California, (1993).
34.K. Takahashi and M. Nei, “Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used,” Mol. Biol. Evol. 17, 1251-1258 (2000).
35.L. KangSeok, V. Shikha, J. SantaLucia Jr and P. R. Cunningham, “In vivo determination of RNA structure-function relationships: analysis of the 790 loop in ribosomal RNA,” J. Mol. Biol. 269, 732-743 (1997).
36.M. Kimura, “A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences,” J. Mol. Evol. 16, 111-120 (1980).
37.N. B. Leontis, E. Westhof, “A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs,” J. Mol. Biol. 283, 571-583 (1998).
38.N. Saitou and M. Nei, “The neighbor-joining method: a new method for reconstructing phylogenetic trees,” Mol. Biol. Evol. 4, 406-425 (1987).
39.P. De Rijk and R. De Wachter, “DCSE, an interactive tool for sequence alignment and secondary structure research,” Comput Appl Biosci. 9, 735-40 (1993).
40.R. Agrawal and R. Srikant, “Fast algorithm for mining association rules in large databases,” In Research Report RJ 9839, IBM Almaden Research Center, San Jose, CA, June, 487-499 (1994).
41.R. Agrawal and R. Srikant, “Mining sequential patterns,” Proc. of the 11th Int'l Conference on Data Engineering, Taipei, Taiwan (1995).
42.R. B. Lyngs, M. Zuker and C. N. S. Pedersen, “Fast evaluation of internal loops in RNA secondary structure prediction,” Bioinformatics 15, 440-445 (1999).
43.R. B. Lyngs, M. Zuker and C. N. S. Pedersen, “Internal loops in RNA secondary structure prediction,” In RECOMB99: Proceedings of the Third Annual International Conference on Computational Molecular Biology, 260-267 (1999).
44.R. R. Gutell, “Collection of small subunit (16S- and 16S-like) ribosomal RNA structures,” Nuc. Acids. Res., 22, 3502—3507 (1994).
45.R. R. Gutell, J. J. Cannone, D. Konings and D. Gautheret, “Predicting U-turns in ribosomal RNA with comparative sequence analysis,” J. Mol. Biol. 300, 791-803.
46.S. R. Eddy and R. Durbin, “RNA sequence analysis using covariance models,” Nucleic Acids Res. 22, 2079-88 (1994).
47.S. V. Morosyuk, K. Lee, J. SantaLucia Jr, P. R. Cunningham, “Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA: analysis of the stem nucleotides,” J. Mol. Biol. 300, 113-126 (2000).
48.T. H. Jukes, C. R. Cantor, “Evolution of protein molecules,” In: Munro HH (ed) Mammalian protein metabolism. New York: Academic Press, 21-132 (1969).
49.Y. Van de Peer, E. Robbrecht, S. de Hoog, A. Caers, P. De Rijk and R. De Wachter, “Database on the structure of small subunit ribosomal RNA,” Nucleic Acids Res. 27, 179-183 (1999).
50.Y. Van de Peer, G. Van de Auwera and R. De Wachter, “The evolution of stramenopiles and alveolates as derived by "substitution rate calibration" of small ribosomal subunit RNA,” J. Mol. Evol. 42, 201-210 (1996).
51.Y. Van de Peer, J. M. Neefs, P. De Rijk and R. De Wachter, “Evolution of eukaryotes as deduced from small ribosomal subunit RNA sequences,” In Biochem. Syst. Ecol. 21, 43-55 (1993b).
52.Y. Van de Peer, P. De Rijk, J. Wuyts, T. Winkelmans and R. De Wachter, “The european small subunit ribosomal RNA database,” Nucleic Acids Res. 28, 175-176 (2000).
53.Y. Van de Peer, S. Chapelle and R. De Wachter, “A quantitative map of nucleotide substitution rates in bacterial rRNA,” Nucleic Acids Research 24, 3381-3391 (1996).
54.Z. Yang, “Phylogenetic analysis using parsimony and likelihood methods,” J. Mol. Evol. 42, 294-307 (1994).

指導教授

洪炯宗(Jorng-Tzong Horng)

審核日期

2001-7-5

推文