RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Universitaetsstrasse 25, Bielefeld, Germany.
BMC Bioinformatics. 2020 Mar 18;21(1):113. doi: 10.1186/s12859-020-3434-9.
RNA-binding proteins interact with their target RNAs at specific sites. These binding sites can be determined genome-wide through individual nucleotide resolution crosslinking immunoprecipitation (iCLIP). Subsequently, the binding sites have to be visualized. So far, no visualization tool exists that is easily accessible but also supports restricted access so that data can be shared among collaborators.
Here we present SEQing, a customizable interactive dashboard to visualize crosslink sites on target genes of RNA-binding proteins that have been obtained by iCLIP. Moreover, SEQing supports RNA-seq data that can be displayed in a different window tab. This allows, e.g. crossreferencing the iCLIP data with genes differentially expressed in mutants of the RBP and thus obtain some insights into a potential functional relevance of the binding sites. Additionally, detailed information on the target genes can be incorporated in another tab.
SEQing is written in Python3 and runs on Linux. The web-based access makes iCLIP data easily accessible, even with mobile devices. SEQing is customizable in many ways and has also the option to be secured by a password. The source code is available at https://github.com/malewins/SEQing.
RNA 结合蛋白在特定位置与它们的靶 RNA 相互作用。这些结合位点可以通过单个核苷酸分辨率交联免疫沉淀（iCLIP）在全基因组范围内确定。随后，必须对这些结合位点进行可视化。到目前为止，还没有一个易于访问但也支持受限访问的可视化工具，以便数据可以在合作者之间共享。
在这里，我们介绍了 SEQing，这是一个可定制的交互式仪表板，用于可视化通过 iCLIP 获得的 RNA 结合蛋白靶基因上的交联位点。此外，SEQing 还支持 RNA-seq 数据，可以在不同的窗口选项卡中显示。这允许例如，将 iCLIP 数据与 RBP 突变体中差异表达的基因进行交叉引用，从而获得关于结合位点潜在功能相关性的一些见解。此外，还可以在另一个选项卡中包含有关靶基因的详细信息。
SEQing 是用 Python3 编写的，在 Linux 上运行。基于网络的访问使得 iCLIP 数据即使在移动设备上也易于访问。SEQing 可以通过多种方式进行定制，也可以选择通过密码进行保护。源代码可在 https://github.com/malewins/SEQing 上获得。
