Improving RNA secondary structure prediction using direct coupling analysis

doi:10.1088/1674-1056/ab889d

中国物理B ›› 2020, Vol. 29 ›› Issue (7): 78702-078702.doi: 10.1088/1674-1056/ab889d

所属专题： SPECIAL TOPIC — Modeling and simulations for the structures and functions of proteins and nucleic acids

Improving RNA secondary structure prediction using direct coupling analysis

Xiaoling He(何小玲), Jun Wang(王军), Jian Wang(王剑), Yi Xiao(肖奕)

School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China

收稿日期:2020-03-23 修回日期:2020-04-08 出版日期:2020-07-05 发布日期:2020-07-05
通讯作者: Yi Xiao E-mail:yxiao@hust.edu.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant No. 31570722).

Improving RNA secondary structure prediction using direct coupling analysis

Xiaoling He(何小玲), Jun Wang(王军), Jian Wang(王剑), Yi Xiao(肖奕)

School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China

Received:2020-03-23 Revised:2020-04-08 Online:2020-07-05 Published:2020-07-05
Contact: Yi Xiao E-mail:yxiao@hust.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant No. 31570722).

摘要/Abstract

摘要： Secondary structures of RNAs are the basis of understanding their tertiary structures and functions and so their predictions are widely needed due to increasing discovery of noncoding RNAs. In the last decades, a lot of methods have been proposed to predict RNA secondary structures but their accuracies encountered bottleneck. Here we present a method for RNA secondary structure prediction using direct coupling analysis and a remove-and-expand algorithm that shows better performance than four existing popular multiple-sequence methods. We further show that the results can also be used to improve the prediction accuracy of the single-sequence methods.

关键词: RNA secondary structure, structure prediction, direct coupling analysis

Abstract: Secondary structures of RNAs are the basis of understanding their tertiary structures and functions and so their predictions are widely needed due to increasing discovery of noncoding RNAs. In the last decades, a lot of methods have been proposed to predict RNA secondary structures but their accuracies encountered bottleneck. Here we present a method for RNA secondary structure prediction using direct coupling analysis and a remove-and-expand algorithm that shows better performance than four existing popular multiple-sequence methods. We further show that the results can also be used to improve the prediction accuracy of the single-sequence methods.

Key words: RNA secondary structure, structure prediction, direct coupling analysis

中图分类号: (Secondary structure)

87.15.bd

87.14.gn (RNA) 87.15.A- (Theory, modeling, and computer simulation)

何小玲, 王军, 王剑, 肖奕. Improving RNA secondary structure prediction using direct coupling analysis[J]. 中国物理B, 2020, 29(7): 78702-078702.

Xiaoling He(何小玲), Jun Wang(王军), Jian Wang(王剑), Yi Xiao(肖奕). Improving RNA secondary structure prediction using direct coupling analysis[J]. Chin. Phys. B, 2020, 29(7): 78702-078702.

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Improving RNA secondary structure prediction using direct coupling analysis

Improving RNA secondary structure prediction using direct coupling analysis

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