DrawRNA2D: Spring-mass system for RNA secondary structure visualization including pseudoknots

• Main Authors: Yung-Tsun Tung, 董勇村
• Other Authors: 洪炯宗
• Format: Others
• Language: zh-TW
• Published: 2007
• Online Access: http://ndltd.ncl.edu.tw/handle/23532542384829475784

碩士 === 國立中央大學 === 資訊工程學系碩士在職專班 === 95 === 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.