RNA pseudoknot prediction based on local structure interaction

被引：0

作者：

Liu, Yuan-Ning ^{[1
,2
]}

Ai, Lu-Lu ^{[1
,2
]}

Duan, Yun-Na ^{[1
,2
]}

Li, Zhi ^{[3
]}

Tian, Ming-Yao ^{[4
]}

Zhang, Hao ^{[1
,2
]}

机构：

[1] College of Computer Science and Technology, Jilin University, Changchun

[2] Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun

[3] College of Applied Technique, Changchun University of Science and Technology, Changchun

[4] Military Veterinary Institute, Academy of Military Medical Science, Changchun

来源：

Jilin Daxue Xuebao (Gongxueban)/Journal of Jilin University (Engineering and Technology Edition) | 2015年 / 45卷 / 02期

关键词：

Computer application; Minimal free energy; Pairing interaction; Pseudoknot; RNA secondary structure;

D O I：

10.13229/j.cnki.jdxbgxb201502041

中图分类号：

学科分类号：

摘要：

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. ©, 2015, Editorial Board of Jilin University. All right reserved.

引用

页码：613 / 618

页数：5

共 10 条

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