Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614 Poznan, Poland.
Nucleic Acids Res. 2020 Jul 2;48(W1):W292-W299. doi: 10.1093/nar/gkaa396.
RNA molecules play key roles in all living cells. Knowledge of the structural characteristics of RNA molecules allows for a better understanding of the mechanisms of their action. RNA chemical probing allows us to study the susceptibility of nucleotides to chemical modification, and the information obtained can be used to guide secondary structure prediction. These experimental results can be analyzed using various computational tools, which, however, requires additional, tedious steps (e.g., further normalization of the reactivities and visualization of the results), for which there are no fully automated methods. Here, we introduce RNAProbe, a web server that facilitates normalization, analysis, and visualization of the low-pass SHAPE, DMS and CMCT probing results with the modification sites detected by capillary electrophoresis. RNAProbe automatically analyzes chemical probing output data and turns tedious manual work into a one-minute assignment. RNAProbe performs normalization based on a well-established protocol, utilizes recognized secondary structure prediction methods, and generates high-quality images with structure representations and reactivity heatmaps. It summarizes the results in the form of a spreadsheet, which can be used for comparative analyses between experiments. Results of predictions with normalized reactivities are also collected in text files, providing interoperability with bioinformatics workflows. RNAProbe is available at https://rnaprobe.genesilico.pl.
RNA 分子在所有活细胞中都发挥着关键作用。了解 RNA 分子的结构特征有助于更好地理解它们的作用机制。RNA 化学探测使我们能够研究核苷酸对化学修饰的敏感性，并且获得的信息可用于指导二级结构预测。可以使用各种计算工具分析这些实验结果，但是，这需要额外的、繁琐的步骤（例如，进一步归一化反应性并可视化结果），而这些步骤没有完全自动化的方法。在这里，我们引入了 RNAProbe，这是一个网络服务器，可简化低通 SHAPE、DMS 和 CMCT 探测结果的归一化、分析和可视化，并对毛细管电泳检测到的修饰位点进行分析。RNAProbe 自动分析化学探测输出数据，将繁琐的手动工作变成了一分钟的任务。RNAProbe 基于成熟的方案进行归一化，利用公认的二级结构预测方法，并生成带有结构表示和反应性热图的高质量图像。它以电子表格的形式总结结果，可用于实验之间的比较分析。归一化反应性预测的结果也以文本文件的形式收集，与生物信息学工作流程具有互操作性。RNAProbe 可在 https://rnaprobe.genesilico.pl 上获得。
