RNA secondary structure prediction is widely used for developing hypotheses about the structures of RNA sequences, and structure can provide insight about RNA function. The accuracy of structure prediction is known to be improved using experimental mapping data that provide information about the pairing status of single nucleotides, and these data can now be acquired for whole transcriptomes using high-throughput sequencing. Prior methods for using these experimental data focused on predicting structures for sequences assuming that they populate a single structure. Most RNAs populate multiple structures, however, where the ensemble of strands populates structures with different sets of canonical base pairs. The focus on modeling single structures has been a bottleneck for accurately modeling RNA structure. In this work, we introduce Rsample, an algorithm for using experimental data to predict more than one RNA structure for sequences that populate multiple structures at equilibrium. We demonstrate, using SHAPE mapping data, that we can accurately model RNA sequences that populate multiple structures, including the relative probabilities of those structures. This program is freely available as part of the RNAstructure software package.

中文翻译：

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使用SHAPE映射数据建模RNA二级结构折叠整合体

RNA二级结构预测已广泛用于开发有关RNA序列结构的假设，并且结构可以提供有关RNA功能的见解。已知使用提供有关单个核苷酸配对状态信息的实验作图数据可以提高结构预测的准确性，并且现在可以使用高通量测序获得整个转录组的这些数据。使用这些实验数据的现有方法着重于预测序列的结构，前提是假设它们构成单个结构。但是，大多数RNA会构成多个结构，在此，多股链会以不同的规范碱基对集合构成结构。对单个结构进行建模的重点一直是精确建模RNA结构的瓶颈。在这项工作中，我们介绍Rsample，一种算法，用于使用实验数据预测一个以上处于平衡状态的多个结构的RNA结构。我们使用SHAPE映射数据证明，我们可以准确地模拟填充多个结构的RNA序列，包括这些结构的相对概率。该程序可作为RNAstructure软件包的一部分免费获得。