應用彈簧粒子系統於RNA二級結構包含偽結的視覺化

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董勇村(Yung-Tsun Tung) 查詢紙本館藏

畢業系所

資訊工程學系在職專班

論文名稱

應用彈簧粒子系統於RNA二級結構包含偽結的視覺化
(DrawRNA2D: Spring-mass system for RNA secondary structure visualization including pseudoknots)

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摘要(中)

RNA二級結構的視覺化對RNA的功能分析有相當大的幫助。一個良好的RNA二級結構呈現工具，將有助於使用者瞭解RNA之整體結構與其功能。因此如何開發一個讓能夠呈現RNA二級結構影像，並且能連結其它生物資訊系統的工具程式，是個很重要的研究方向。另一方面，目前的RNA二級結構繪製程式大都是使用幾何學的公式去繪製結構影像，這種方式在繪製偽結(Pseudoknots)時需依照其偽結結構分類套用不同模版處理，因此並無法呈現易於辨識的完整結構。為了解決上述的問題，本篇論文應用彈簧粒子系統去模擬RNA二級結構的摺疊過程，以產生較容易辨識的結構影像。我們實際使用此演算法建立了一個系統—DrawRNA2D，此系統提供了展示RNA二級結構摺疊過程的視覺化工具，並可使用此工具控制或移動RNA二級結構影像，同時此系統也提供了多種方式讓使用者或其它程式透過網際網路呼叫繪製RNA二級結構的功能。最後我們將DrawRNA2D系統與目前最常被使用的PseudoViewer系統作比較，並說明其兩者的差異。

摘要(英)

RNA secondary structure visualization is very useful for RNA function analysis. A good RNA secondary structure visualization tool can assist user to understand the RNA structure and function. So how to develop a program component which draws RNA secondary structure is an important research direction. On the other hand, current RNA secondary structure visualization programs are mostly use the geometry formula to draw the structure. The method must apply different structure template when draws the pseudoknots, so it is unable to present a complete structure which is easy to identify. In order to solve the above problems, we present an algorithm to draws the RNA secondary structure. The algorithm uses spring-mass system to simulate the formation of RNA secondary structure folding, and generate the structure image which is easy to identify. We use the algorithm to implement a system-DrawRNA2D. The system provides a tool which is able to simulate the formation of RNA secondary structure folding, and also let user can use the tool to manipulate the RNA secondary structure. In addition, the system provides the various methods to let other program can use the function which draws RNA secondary structure via Internet. Finally we compare DrawRNA2D with PseudoViewer, and explain the difference.

關鍵字(中)

★ 彈簧粒子系統
★ 偽結
★ RNA二級結構

關鍵字(英)

★ RNA secondary structure
★ pseudoknots

論文目次

中文摘要................................................iii
英文摘要................................................iii
目錄....................................................iii
圖目錄..................................................iii
第一章概述.............................................1
第二章演算法...........................................4
2.1 粒子的模擬........................................4
2.2 彈簧的模擬........................................5
2.3 即時模擬..........................................9
2.4 力場..............................................11
2.5 影像調整..........................................12
2.6 整體運算流程......................................13
第三章系統實作.........................................15
3.1 軟體架構..........................................15
3.2 系統架構..........................................17
3.3 Web應用程式.......................................20
3.4 Web服務...........................................20
3.5 Web服務的輸入.....................................21
3.6 Web服務的輸出.....................................23
第四章結果.............................................24
4.1 一般莖環結構的模擬................................26
4.2 各種偽結結構的模擬................................27
4.3 結構的控制........................................32
4.4 與PseudoViewer的比較.............................33
4.5 Web服務客戶端.....................................34
第五章結論.............................................36
參考文獻................................................38

參考文獻

[1]Zuker, M., 2003. "Mfold web server for nucleic acid folding and hybridization prediction", Nucleic Acids Research, 31,3406-3415.
[2]Wiese, K. C. & Glen, E., 2003. "A permutation-based genetic algorithm for the RNA folding problem: a critical look at selection strategies, crossover operators, and representation issues",BioSystems - Special Issue on Computational Intelligence in Bioinformatics, 41,72-29.
[3]Wiese, K. C. & Hendriks, A., 2006. "Comparison of P-RnaPredict and mfold - algorithms for RNA secondary structure prediction",Bioinformatics, 22(8),934-942.
[4]Major, F. & Griffey, R., 2001. "Computational methods for RNA structure determination", Current Opinion in Structural Biology,11,282-286.
[5]Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, L.S., Tacker, M. & Schuster, P., 1994. "Fast Folding and Comparison of RNA Secondary Structures", Monatsh.Chem., 125,167-188.
[6]Reeder,J. and Giegerich,R., 2004. "Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics", BMC Bioinformatics, 5,104-115.
[7]Rijk, P.D. & Wachter, R.D., 1997. "RnaViz, a program for the visualisation of RNA secondary structure", Nucleic Acids Research, 25,4679-4684.
[8]Rijk, P.D., Wuyts, J. & Wachter, R.D. "RnaViz 2: an improved representation of RNA secondary structure," Bioinformatics, 2003, 19, 299-300.
[9]Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H. & Westhof, E., 2003. "Tools for the automatic identification and classification of RNA base pairs", Nucleic Acids Research, 31,3450-3460.
[10]Han, K.; Lee, Y. & Kim, W., 2002. "PseudoViewer: automatic visualization of RNA pseudoknots", Bioinformatics, 18,S321-S328.
[11]Han, K. & Byun, Y., 2003. "PseudoViewer 2: visualization of RNA pseudoknots of any type", Nucleic Acids Research, 31,3432-3440.
[12]Han, K. & Byun, Y., 2006. "PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures",Nucleic Acids Research, ,34,W416-W422.
[13]Jesper, M., 2003. "LR-spring-mass model for cardiac surgical simulation", Medicine Meets Virtual Reality, 12,256-258.
[14]Feng, J., Ruqin, L. & Yiping, Q., 2006. "Three-dimensional Garment Simulation Based on a Mass-Spring System" ,Textile Research Journal, 76,12-17.
[15]Miyazaki, S., Sugawara, H., Gojobori, T., Tateno Y., 2003. "DNA Data Bank of Japan (DDBJ) in XML", Nucleic Acids Research, 31,13-16.
[16]Kawashima, S., Katayama, T., Sato, Y., Kanehisa, M., 2003. "KEGG API: A Web Service Using SOAP/WSDL to Access the KEGG System", Genome Inform., 14,673-674.
[17]Chen, Y., Kortemme, T., Robertson, T., Baker, D. & Varani, G., 2004. "A new hydrogen-bonding potential for the design of Protein–RNA interactions predicts specific contacts and discriminates decoys", Nucleic Acids Research, 32, 5147-5162.
[18]Jacobson, I., Grady, B. & James, R., 1998. "The Unified Software Development Process", Addison Wesley Longman. ISBN 0-201-57169-2.
[19]van Batenburg, F. H. D., Gultyaev, A. P. & Pleij, C. W. A., 2001. "PseudoBase: structural information on RNA pseudoknots", Nucleic Acids Research, 29,194-195.
[20]Lowe, T. M. & Eddy, S. R., 1997. "tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence", Nucleic Acids Research, 25, 955-964.
[21]Griffiths-Jones, S., Grocock, R. J.,van Dongen, S., Bateman, A. & Enright, A. J., 2006, "miRBase: microRNA sequences, targets and gene nomenclature", Nucleic Acids Research, 34, D140-D144.

指導教授

洪炯宗(Jorng-Tzong Horng)

審核日期

2007-7-19

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