The secondary structure of an RNA is often implicit to its function. Recently, various high-throughput RNA structure probing techniques have been developed to elucidate important RNA structure-function relationships genome-wide. These techniques produce unwieldy experimental data sets that require evaluation with unique computational pipelines. Herein, we present StructureFold2, a user-friendly set of analysis tools that makes precise data processing and detailed downstream analyses of such data sets both available and practical. StructureFold2 processes high-throughput reads sequenced from libraries prepared after experimental probing for reverse transcription (RT) stops generated by chemical modification of RNA at solvent accessible residues. This pipeline is able to analyze reads generated from a variety of structure-probing chemicals (e.g. DMS, glyoxal, SHAPE). Notably, StructureFold2 offers a new fully featured suite of utilities and tools to guide a user through multiple types of analyses. A particular emphasis is placed on analyzing the reactivity patterns of transcripts, complementing their use as folding restraints for predicting RNA secondary structure. StructureFold2 is hosted as a Github repository and is available at (https://github.com/StructureFold2/StructureFold2).

中文翻译：

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StructureFold2：将化学探测数据带入 RNA 结构分析的计算折叠

RNA 的二级结构通常隐含于其功能中。最近，已开发出各种高通量 RNA 结构探测技术来阐明全基因组范围内重要的 RNA 结构-功能关系。这些技术产生了需要使用独特的计算管道进行评估的笨拙的实验数据集。在此，我们介绍 StructureFold2，这是一组用户友好的分析工具，可对此类数据集进行精确的数据处理和详细的下游分析，既可用又实用。StructureFold2 处理从在实验探测逆转录 (RT) 停止后制备的文库中测序的高通量读数，逆转录 (RT) 停止是通过溶剂可及残基处的 RNA 化学修饰产生的。该管道能够分析由各种结构探测化学品（例如 DMS、乙二醛，形状）。值得注意的是，StructureFold2 提供了一套新的功能齐全的实用程序和工具，以指导用户进行多种类型的分析。特别强调分析转录物的反应模式，补充它们作为预测 RNA 二级结构的折叠限制的用途。StructureFold2 作为 Github 存储库托管，可从 (https://github.com/StructureFold2/StructureFold2) 获得。