Predicting a set of minimal free energy RNA secondary structures common to two sequences
Predicting a set of minimal free energy RNA secondary structures common to two sequences
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DOI：
10.1093/bioinformatics/bti349
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发表时间：
2005-05-15
期刊：
影响因子：
5.8
通讯作者：
Mathews, DH
中科院分区：
文献类型：
--
作者：
Mathews, DH
动机：功能来源于结构，因此，需要有预测RNA功能结构的方法。结果：将预测两个未对齐RNA序列共有的最低自由能二级结构的Dynalign算法扩展到预测一组低能结构。可以绘制点图来显示能量增量内结构中的所有碱基对。与使用单一序列的结构预测相比，Dynalign预测更明确的结构；在5S rRNA序列中，能量在最低能量结构20%以内的结构中，使用Dynalign的平均碱基对数为317个，而使用单个序列的平均碱基对数为569个。Dynalign的结构预测也可以根据实验或对比分析进行约束。以灵敏度和阳性预测值来衡量，Dynalign的准确性大于单一序列的预测。
Motivation: Function derives from structure, therefore, there is need for methods to predict functional RNA structures.Results: The Dynalign algorithm, which predicts the lowest free energy secondary structure common to two unaligned RNA sequences, is extended to the prediction of a set of low-energy structures. Dot plots can be drawn to show all base pairs in structures within an energy increment. Dynalign predicts more well-defined structures than structure prediction using a single sequence; in 5S rRNA sequences, the average number of base pairs in structures with energy within 20% of the lowest energy structure is 317 using Dynalign, but 569 using a single sequence. Structure prediction with Dynalign can also be constrained according to experiment or comparative analysis. The accuracy, measured as sensitivity and positive predictive value, of Dynalign is greater than predictions with a single sequence.