Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions.
Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions.
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DOI：
10.1093/nar/gks1283
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发表时间：
2013-03-01
影响因子：
14.9
通讯作者：
Heitsch CE
中科院分区：
文献类型：
--
作者：
Sükösd Z;Swenson MS;Kjems J;Heitsch CE
RNA结构测定的最新进展包括使用来自高通量探测实验的数据来提高热力学预测的准确性。我们评估的程度和性质的改进数据导向的预测不同的16 S/18 S核糖体序列使用随机模型的实验SHAPE数据。1000个数据导向预测的平均准确度总是比原始的最小自由能（MFE）结构更高。然而，改善的量随序列而变化，表现出与MFE精度的相关性。对这种相关性的进一步分析表明，准确的MFE碱基对通常在数据导向预测中被保留，而不准确的则不然。因此，共同碱基对的阳性预测值始终高于定向预测准确度。最后，我们确认序列的热力学预测的方向性的依赖关系，并调查潜在的更大的准确性的改进，在最差的测试序列。
Recent advances in RNA structure determination include using data from high-throughput probing experiments to improve thermodynamic prediction accuracy. We evaluate the extent and nature of improvements in data-directed predictions for a diverse set of 16S/18S ribosomal sequences using a stochastic model of experimental SHAPE data. The average accuracy for 1000 data-directed predictions always improves over the original minimum free energy (MFE) structure. However, the amount of improvement varies with the sequence, exhibiting a correlation with MFE accuracy. Further analysis of this correlation shows that accurate MFE base pairs are typically preserved in a data-directed prediction, whereas inaccurate ones are not. Thus, the positive predictive value of common base pairs is consistently higher than the directed prediction accuracy. Finally, we confirm sequence dependencies in the directability of thermodynamic predictions and investigate the potential for greater accuracy improvements in the worst performing test sequence.
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14.9
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LE, SY;CHEN, JH;MAIZEL, JV
通讯作者：
MAIZEL, JV
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