School for Life Science and Technology, Hanze University of Applied Sciences, 9747 AS Groningen, The Netherlands.
Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands.
Nucleic Acids Res. 2024 Jul 5;52(W1):W362-W367. doi: 10.1093/nar/gkae348.
RNA molecules perform a variety of functions in cells, many of which rely on their secondary and tertiary structures. Chemical probing methods coupled with high-throughput sequencing have significantly accelerated the mapping of RNA structures, and increasingly large datasets of transcriptome-wide RNA chemical probing data are becoming available. Analogously to what has been done for decades in the protein world, this RNA structural information can be leveraged to aid the discovery of structural similarity to a known RNA (or RNA family), which, in turn, can inform about the function of transcripts. We have previously developed SHAPEwarp, a sequence-agnostic method for the search of structurally homologous RNA segments in a database of reactivity profiles derived from chemical probing experiments. In its original implementation, however, SHAPEwarp required substantial computational resources, even for moderately sized databases, as well as significant Linux command line know-how. To address these limitations, we introduce here SHAPEwarp-web, a user-friendly web interface to rapidly query large databases of RNA chemical probing data for structurally similar RNAs. Aside from featuring a completely rewritten core, which speeds up by orders of magnitude the search inside large databases, the web server hosts several high-quality chemical probing databases across multiple species. SHAPEwarp-web is available from https://shapewarp.incarnatolab.com.
RNA 分子在细胞中执行多种功能，其中许多功能依赖于它们的二级和三级结构。化学探测方法与高通量测序相结合，极大地加速了 RNA 结构的绘制，越来越多的转录组范围的 RNA 化学探测数据数据集变得可用。类似于几十年来在蛋白质领域所做的那样，这种 RNA 结构信息可以用来帮助发现与已知 RNA（或 RNA 家族）的结构相似性，这反过来又可以提供关于转录本功能的信息。我们之前开发了 SHAPEwarp，这是一种在化学探测实验衍生的反应性图谱数据库中搜索结构同源 RNA 片段的无序列依赖性方法。然而，在最初的实现中，SHAPEwarp 需要大量的计算资源，即使对于中等大小的数据库也是如此，并且需要对 Linux 命令行有相当的了解。为了解决这些限制，我们在这里引入了 SHAPEwarp-web，这是一个用户友好的网络界面，可以快速查询大型 RNA 化学探测数据库，以寻找结构相似的 RNA。除了具有完全重写的核心外，该核心将在大型数据库中的搜索速度提高了几个数量级，该网络服务器还托管了多个跨多种物种的高质量化学探测数据库。SHAPEwarp-web 可从 https://shapewarp.incarnatolab.com 获得。
