Italian Institute for Genomic Medicine (IIGM), Via Nizza 52, 10126 Torino, Italy.
Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, Torino, Italy.
Nucleic Acids Res. 2018 Sep 19;46(16):e97. doi: 10.1093/nar/gky486.
RNA is emerging as a key regulator of a plethora of biological processes. While its study has remained elusive for decades, the recent advent of high-throughput sequencing technologies provided the unique opportunity to develop novel techniques for the study of RNA structure and post-transcriptional modifications. Nonetheless, most of the required downstream bioinformatics analyses steps are not easily reproducible, thus making the application of these techniques a prerogative of few laboratories. Here we introduce RNA Framework, an all-in-one toolkit for the analysis of most NGS-based RNA structure probing and post-transcriptional modification mapping experiments. To prove the extreme versatility of RNA Framework, we applied it to both an in-house generated DMS-MaPseq dataset, and to a series of literature available experiments. Notably, when starting from publicly available datasets, our software easily allows replicating authors' findings. Collectively, RNA Framework provides the most complete and versatile toolkit to date for a rapid and streamlined analysis of the RNA epistructurome. RNA Framework is available for download at: http://www.rnaframework.com.
RNA 正在成为众多生物过程的关键调节因子。尽管几十年来对其研究一直难以捉摸，但最近高通量测序技术的出现为研究 RNA 结构和转录后修饰提供了独特的机会。尽管如此，大多数需要的下游生物信息学分析步骤都不容易重现，因此这些技术的应用仅限于少数几个实验室。在这里，我们介绍 RNA 框架，这是一种用于分析大多数基于 NGS 的 RNA 结构探测和转录后修饰图谱实验的一体化工具包。为了证明 RNA 框架的极端多功能性，我们将其应用于内部生成的 DMS-MaPseq 数据集和一系列可用的文献实验。值得注意的是，当从公开可用的数据集开始时，我们的软件可以轻松复制作者的发现。总的来说，RNA 框架提供了迄今为止最完整和多功能的工具包，可用于快速简化 RNA 结构组学的分析。RNA 框架可在以下网址下载：http://www.rnaframework.com。
