Computer Engineering and Applications ›› 2012, Vol. 48 ›› Issue (11): 26-31.

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Dynamic generation method for calculating genus of RNA secondary structure graph

GAO Shile1, WANG Qizhao2   

  1. 1.Department of Information Management & System, Huaqiao University, Quanzhou, Fujian 362021, China
    2.Institute of Molecular Medicine, Huaqiao University, Quanzhou, Fujian 362021, China
  • Online:2012-04-11 Published:2012-04-16



  1. 1.华侨大学 信息管理与信息系统系,福建 泉州 362021
    2.华侨大学 分子药物学研究所,福建 泉州 362021

Abstract: A dynamic generation method is presented based on arc graph grammars of Rivas and Eddy(R&E) RNA secondary class to calculate the genus of RNA secondary structure graph. Comparing with the determinant method for calculating genus, the presented method mainly has two advantages:the first one is the improvement of the efficiency of genus calculation, the second one is the generation of the mini-genus graphs of RNA secondary structures.

Key words: pseudoknots, RNA secondary structures, topological classification, genus

摘要: 基于Rivas和Eddy(R&E)RNA二级结构类的图语法,提出了一种计算RNA二级结构图亏格的动态生成算法。与已有的基于判定的亏格计算方法相比,该算法的优点主要有两点:一是提高了计算亏格的效率,二是可以实现枚举小亏格RNA二级结构图。

关键词: 假结, RNA二级结构, 拓扑分类, 亏格