Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
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DOI：
10.1261/rna.7650904
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发表时间：
2004-08-01
期刊：
影响因子：
4.5
通讯作者：
Mathews, DH
中科院分区：
文献类型：
--
作者：
Mathews, DH
本文提出了一种RNA二级结构配分函数的计算方法，该方法使用当前最近邻参数集来计算37°c的构象自由能，包括同轴堆叠。对于多样化的RNA序列数据库，预测最小自由能结构中由配分函数预测的碱基对配对概率高的碱基对对于已知碱基对具有显著更高的正预测值。例如，当只考虑概率在0.99及以上的碱基对时，平均阳性预测值从65.8%增加到91.0%。碱基对预测的质量也可以通过添加实验确定的约束条件来提高，包括酶裂解、黄素单核苷酸裂解和化学修饰。与配对概率较低的碱基对相比，预测的二级结构可以用颜色标注来证明具有高概率的配对。
A partition function calculation for RNA secondary structure is presented that uses a current set of nearest neighbor parameters for conformational free energy at 37degreesC, including coaxial stacking. For a diverse database of RNA sequences, base pairs in the predicted minimum free energy structure that are predicted by the partition function to have high base pairing probability have a significantly higher positive predictive value for known base pairs. For example, the average positive predictive value, 65.8%, is increased to 91.0% when only base pairs with probability of 0.99 or above are considered. The quality of base pair predictions can also be increased by the addition of experimentally determined constraints, including enzymatic cleavage, flavin mononucleotide cleavage, and chemical modification. Predicted secondary structures can be color annotated to demonstrate pairs with high probability that are therefore well determined as compared to base pairs with lower probability of pairing.