Secondary structure prediction of interacting RNA molecules
Secondary structure prediction of interacting RNA molecules
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DOI：
10.1016/j.jmb.2004.10.082
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发表时间：
2005-02-04
影响因子：
5.6
通讯作者：
Condon, A
中科院分区：
文献类型：
--
作者：
Andronescu, M;Zhang, ZC;Condon, A
预测两个或多个相互作用的核酸分子的二级结构的计算工具对于了解核酶功能的机制、确定寡核苷酸引物与其靶标的亲和力以及设计良好的反义寡核苷酸、新型核酶、DNA密码字或纳米结构是有用的。在这里，我们介绍了预测两个或多个核酸分子的最小自由能无伪结二级结构的新算法，以及预测两个核酸分子的替代低能(次优)二级结构的新算法。我们从文献中对针对相互作用的RNA分子的二级结构的预测提供了全面的分析。我们的工具分析了17个不形成伪结点的长达200个核苷酸的序列，结果表明，对于最小自由能预测，它们平均有79%的准确率。当在100个次优折叠中取最优时，平均准确率提高到91%。随着序列长度的增加以及伪结点和三级相互作用数量的增加，精确度降低。我们的算法扩展了Zuker&Stiegler的二级结构预测的自由能最小化算法和Wuchty等人的次优折叠算法。我们算法的实现可以在MulfiRNAFold(http://www.rnasoff.ca/download.html).)包中免费获得(C)2004爱思唯尔有限公司。所有比赛已预留。
Computational tools for prediction of the secondary structure of two or more interacting nucleic acid molecules are useful for understanding mechanisms for ribozyme function, determining the affinity of an oligonucleotide primer to its target, and designing good antisense oligonucleotides, novel ribozymes, DNA code words, or nanostructures. Here, we introduce new algorithms for prediction of the minimum free energy pseudoknot-free secondary structure of two or more nucleic acid molecules, and for prediction of alternative low-energy (sub-optimal) secondary structures for two nucleic acid molecules. We provide a comprehensive analysis of our predictions against secondary structures of interacting RNA molecules drawn from the literature. Analysis of our tools on 17 sequences of up to 200 nucleotides that do not form pseudoknots shows that they have 79% accuracy, on average, for the minimum free energy predictions. When the best of 100 sub-optimal foldings is taken, the average accuracy increases to 91%. The accuracy decreases as the sequences increase in length and as the number of pseudoknots and tertiary interactions increases. Our algorithms extend the free energy minimization algorithm of Zuker & Stiegler for secondary structure prediction, and the sub-optimal folding algorithm by Wuchty et al. Implementations of our algorithms are freely available in the package MulfiRNAFold (http://www.rnasoff.ca/download.html). (C) 2004 Elsevier Ltd. All fights reserved.