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RNAProbe: a web server for normalization and analysis of RNA structure probing data.
Nucleic Acids Research ( IF 16.6 ) Pub Date : 2020-06-06 , DOI: 10.1093/nar/gkaa396
Tomasz K Wirecki 1 , Katarzyna Merdas 1 , Agata Bernat 1 , Michał J Boniecki 1 , Janusz M Bujnicki 1, 2 , Filip Stefaniak 1
Affiliation  

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.

中文翻译:

RNAProbe:用于标准化和分析RNA结构探测数据的Web服务器。

RNA分子在所有活细胞中都起着关键作用。了解RNA分子的结构特征可以更好地了解其作用机理。RNA化学探测使我们能够研究核苷酸对化学修饰的敏感性,并且所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来分析这些实验结果,但是,这需要其他繁琐的步骤(例如,对反应性进行进一步的标准化和结果的可视化),而这些方法还没有完全自动化的方法。在这里,我们介绍了RNAProbe,这是一个网络服务器,可通过毛细管电泳检测的修饰位点,促进低通SHAPE,DMS和CMCT探测结果的标准化,分析和可视化。RNAProbe自动分析化学探测输出数据,并将繁琐的手工工作变成一分钟的任务。RNAProbe基于完善的协议进行归一化,利用公认的二级结构预测方法,并生成具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了结果,可用于实验之间的比较分析。具有标准化反应性的预测结果也收集在文本文件中,从而提供了与生物信息学工作流程的互操作性。可从https://rnaprobe.genesilico.pl获得RNAProbe。利用公认的二级结构预测方法,并生成具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了结果,可用于实验之间的比较分析。具有标准化反应性的预测结果也收集在文本文件中,从而提供了与生物信息学工作流程的互操作性。可从https://rnaprobe.genesilico.pl获得RNAProbe。利用公认的二级结构预测方法,并生成具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了结果,可用于实验之间的比较分析。具有标准化反应性的预测结果也收集在文本文件中,从而提供了与生物信息学工作流程的互操作性。可从https://rnaprobe.genesilico.pl获得RNAProbe。提供与生物信息学工作流程的互操作性。可从https://rnaprobe.genesilico.pl获得RNAProbe。提供与生物信息学工作流程的互操作性。可从https://rnaprobe.genesilico.pl获得RNAProbe。
更新日期:2020-06-27
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