基于局部结构交互的RNA假结预测  

RNA pseudoknot prediction based on local structure interaction

作　　者：刘元宁[1,2] 艾露露[1,2] 段云娜[1,2] 李誌[3] 田明尧[4] 张浩[1,2] 

机构地区：[1]吉林大学计算机科学与技术学院,长春130012 [2]吉林大学符号计算与知识工程教育部重点实验室,长春130012 [3]长春理工大学应用技术学院,长春130022 [4]军事医学科学院军事兽医研究所,长春130122

出　　处：《吉林大学学报（工学版）》2015年第2期613-618,共6页Journal of Jilin University:Engineering and Technology Edition

基　　金：国家自然科学基金项目(60971089)

摘　　要：基于RNA局部结构间的交互作用,提出一种含假结的RNA二级结构预测新方法LIFold。对给定的RNA序列,首先通过能量计算得到不含假结的能量最优结构,然后应用局部结构交互配对生成假结茎区,在已得到的最优结构基础上构建含假结的能量计算模型,最后通过优化算法得到含假结的RNA二级结构。应用该方法基于HotKnots测试数据的敏感性和阳性预测值(PPV)分别达到84%和80%,基于PseudoBase数据库测试数据的敏感性和阳性预测值分别达到78%和73%,与HotKnots、ILM、PknotsRG、IPknot及FlexStem等知名软件相比较,准确率均有所提高。According to the interaction between local structures of RNA,a new algorithm,named LIFold,is presented to predict RNA secondary structure with pseudoknot.For a given RNA sequence,first,the optimal RNA secondary structure without pseudoknot is generated based on the method of free energy calculation.Then,the pseudoknot stems are obtained using local structure pairing interaction,and an energy calculation model with pseudoknot is established on the basis of the optimal structure.Finally,the RNA secondary structure with pseudoknot is obtained using optimization algorithm.Using the test data of HotKnots,the sensitivity and Positive Predict Value（PPV）reach 84% and 80% respectively.Using the test data based on PseudoBase database,the sensitivity and PPV reach 78% and 73% respectively.Comparing to HotKnots,ILM,PknotsRG IPknot and FlexStem softwares,the accuracy of the proposed algorithm,LIfold,is higher.

关 键 词：计算机应用 RNA二级结构 假结 最小自由能 交互配对 

分 类 号：TP399[自动化与计算机技术—计算机应用技术]