基于堆积协变信息和最小自由能预测含伪结的RNA二级结构.pdfVIP

生 物 工 程 学 报 Chin J Biotech 2008, April 25; 24(4): 659-664 Chinese Journal of Biotechnology ISSN 1000-3061 cjb@ © 2008 Institute of Microbiology, CAS CSM, All rights reserved 研究报告 RNA 杨金伟, 骆志刚, 方小永, 王金华, 唐可成 , 410073 : RNA 伪结预测是RNA 研究的一个难点问题。文中提出一种基于堆积协变信息与最小自由能的RNA 伪结预测 方法。该方法使用已知结构的 RNA 比对序列(ClustalW 比对和结构比对)测试此方法, 侧重考虑相邻碱基对之间相互作 用形成的堆积协变信息, 并结合最小自由能方法对碱基配对综合评分, 通过逐步迭代求得含伪结的 RNA 二级结构。结 果表明, 此方法能正确预测伪结, 其平均敏感性和特异性优于参考算法, 并且结构比对的预测性能比 ClustalW 比对的 预测性能更加稳定。文中同时讨论了不同协变信息权重因子对预测性能的影响, 发现权重因子比值在λ 1: λ2=5:1 时, 预 测性能达到最优。 : RNA 二级结构、伪结、堆积协变信息、最小自由能 Predicting RNA Secondary Structures Including Pseudoknots by Covariance with Stacking and Minimum Free Energy Jinwei Yang, Zhigang Luo, Xiaoyong Fang, Jinhua Wang, and Kecheng Tang College of Computer Science, National University of Defense Technology, Changsha 410073, China Abstract: Prediction of RNA secondary structures including pseudoknots is a difficult topic in RNA field. Current predicting methods usually have relatively low accuracy and high complexity. Considering that the stacking of adjacent base pairs is a common feature of RNA secondary structure, here we present a method for predicting pseudoknots based on covariance with stacking and minimum free energy. A new score scheme, which combined stacked covariance with free energy, was used to assess the evaluation of base pair in our method. Based on this score scheme, we utilized an iterative procedure to compute the optimized RNA secondary structure wi