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

NCUIR > College of Electrical Engineering & Computer Science > Executive Master of Computer Science and Information Engineering > Electronic Thesis & Dissertation > Item 987654321/8699

Please use this identifier to cite or link to this item: http://ir.lib.ncu.edu.tw/handle/987654321/8699

Title:	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
Authors:	董勇村;Yung-Tsun Tung
Contributors:	資訊工程學系碩士在職專班
Keywords:	彈簧粒子系統;偽結;RNA二級結構;RNA secondary structure;pseudoknots
Date:	2007-07-09
Issue Date:	2009-09-22 11:33:11 (UTC+8)
Publisher:	國立中央大學圖書館
Abstract:	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。 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.
Appears in Collections:	[Executive Master of Computer Science and Information Engineering] Electronic Thesis & Dissertation

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