东北大学学报（自然科学版）

东北大学学报(自然科学版) ›› 2008, Vol. 29 ›› Issue (10): 1389-1392.DOI: -

• 论著 • 上一篇    下一篇

粗糙集算法在预测RNA保守功能二级结构中的应用

付昊月;张祥德;薛定宇;   

  1. 东北大学信息科学与工程学院;东北大学理学院;
  • 收稿日期:2013-06-22 修回日期:2013-06-22 出版日期:2008-10-15 发布日期:2013-06-22
  • 通讯作者: Fu, H.-Y.
  • 作者简介:-
  • 基金资助:
    辽宁省科学技术基金资助项目(002010)

Rough set algorithm to predict RNA conserved secondary structure

Fu, Hao-Yue (1); Zhang, Xiang-De (2); Xue, Ding-Yu (1)   

  1. (1) School of Information Science and Engineering, Northeastern University, Shenyang 110004, China; (2) School of Sciences, Northeastern University, Shenyang 110004, China
  • Received:2013-06-22 Revised:2013-06-22 Online:2008-10-15 Published:2013-06-22
  • Contact: Fu, H.-Y.
  • About author:-
  • Supported by:
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摘要： 提出了一种预测RNA保守功能二级结构的粗糙集算法.使用粗糙集工具Rosetta软件,在保守结构预测过程的数据挖掘模块中,应用经过整理和离散化的RNA备择碱基对数据生成规则确定出将要出现在同源RNA序列的保守二级结构中的碱基对.将此算法应用在对爱滋病病原体HIV病毒RNA中REV应答元件单元的保守二级结构预测的结果表明,与传统的非数据挖掘算法相比,使用了这种机器学习算法的粗糙集预测方法,使得保守功能结构与野生型结构更加相似,重要的功能结构分支更加清晰明确.

关键词: RNA二级结构, 粗糙集, REV应答元件, 保守结构预测, HIV, Rosetta

Abstract: A rough set algorithm was presented to predict the RNA conserved secondary structure. The date generating rules were made for the collated and discretized alternative RNA base pairs in the date mining modules for the predicting process of conserved structure by using the rough set software Rosetta as a tool. With these rules, the base pairs which will appear in the conserved secondary structure of the homologous RNA sequence were determined. The rough set algorithm was applied to the prediction of the conserved secondary structure of REV responsive element in the RNA of a set of HIV virus, and the results showed that in comparison with the conventional nondate mining algorithm, the prediction by rough set with such a machine learning algorithm used makes the predicted conserved structure more similar to the wild-type structure and the important structural branch more explicit.

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