基于PDB数据库的三个RNA二级结构预测软件评估

刘伟^1,3, 黄伊子^1,3, 李都悦^1,3, 向妍^1,3,周玮^1,2,3

(1.湖南农业大学植物保护学院植物病虫害生物学与防控湖南省重点实验室, 长沙 410128; 2.湖南省烟草公司郴州市公司, 湖南 郴州 423000; 3.湖南农业大学湖南省生物农药与制剂加工工程技术研究中心, 长沙 410128)



摘要:

随着21世纪分子生物学研究的蓬勃发展,RNA二级结构预测成为其中一项重要内容。由于RNA二级结构预测的准确性最为关键,因此寻找高精度且易操作的二级结构预测工具显得非常重要。本文选取三种简单且易操作的二级结构预测软件,先基于PDB数据库收录的318个RNA发夹序列进行二级结构预测,进而通过比较预测结果与实验测定结果进行软件预测性能评估。比较结果显示,RNAstructure为三个软件中性能最优的RNA二级结构预测软件。

关键词:  RNA二级结构  PDB数据库  二级结构预测  准确性

DOI：10.3969/j.issn.1672-5565.2015.01.07

分类号:Q74

基金项目:国家自然科学基金青年项目(31301388)；中国博士后面上项目(2014M562109)；湖南省自然科学基金(14JJ3092)；湖南省科学技术厅科技计划项目(2014GK3046)；湖南农业大学大学生科技创新基金(团委)资助科研项目(18)；湖南农业大学植物保护学院"大学生创新性实验计划项目(SAY1106)。



Evaluation of three RNA secondary structure prediction softwares based on PDB database

LIU Wei^1,3,HUANG Yizi^1,3,LI Douyue^1,3,XIANG Yan^1,3,ZHOU Wei^1,2,3

(1.Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University,Changsha 410128, China; 2.Chenzhou Company of Hunan Tobacco Company, Chenzhou Hunan 423000, China; 3.Hunan Provincial Engineering & Technology Research Center for Biopesticide and Formulation Processing, Hunan Agricultural University, Changsha 410128, China)

Abstract:

With the development of molecular biology in the 21^st century, the prediction of RNA secondary structure has become one of the most important contents in the field. Because the accuracy of RNA secondary structure prediction is crucial, it is very important to look for the secondary structure prediction tool with high precision and easy operation. In this article, three kinds of secondary structure prediction softwares were selected to evaluate their performances. Firstly, we predicted the RNA secondary structures of 318 RNA hairpins collected from PDB database, and then evaluated the performance of the softwares by comparing the predicted results with the experimental ones. Comparison results showed that RNA structure was superior to the other two kinds of softwares in predicting RNA secondary structure.

Key words:  RNA secondary structures  PDB database  Secondary structure prediction  Accuracy