Department of Biochemistry, Stanford University School of Medicine, Stanford CA 94305, USA.
Department of Genetics, Stanford University School of Medicine, Stanford CA 94305, USA.
Nucleic Acids Res. 2018 Jan 4;46(D1):D375-D379. doi: 10.1093/nar/gkx873.
Chemical mapping is a broadly utilized technique for probing the structure and function of RNAs. The volume of chemical mapping data continues to grow as more researchers routinely employ this information and as experimental methods increase in throughput and information content. To create a central location for these data, we established an RNA mapping database (RMDB) 5 years ago. The RMDB, which is available at http://rmdb.stanford.edu, now contains chemical mapping data for over 800 entries, involving 134 000 natural and engineered RNAs, in vitro and in cellulo. The entries include large data sets from multidimensional techniques that focus on RNA tertiary structure and co-transcriptional folding, resulting in over 15 million residues probed. The database interface has been redesigned and now offers interactive graphical browsing of structural, thermodynamic and kinetic data at single-nucleotide resolution. The front-end interface now uses the force-directed RNA applet for secondary structure visualization and other JavaScript-based views of bar graphs and annotations. A new interface also streamlines the process for depositing new chemical mapping data to the RMDB.
化学绘图是一种广泛用于探测 RNA 结构和功能的技术。随着越来越多的研究人员常规地使用这些信息，以及实验方法在通量和信息量方面的增加，化学绘图数据的数量持续增长。为了创建这些数据的中心位置，我们在 5 年前建立了一个 RNA 绘图数据库（RMDB）。RMDB 可在 http://rmdb.stanford.edu 上获得，现在包含了超过 800 个条目、涉及 134000 个天然和工程 RNA 的化学绘图数据，包括来自专注于 RNA 三级结构和共转录折叠的多维技术的大型数据集，总共探测了超过 1500 万个残基。数据库界面已经重新设计，现在提供了交互式图形浏览，可按单个核苷酸分辨率查看结构、热力学和动力学数据。前端界面现在使用力导向 RNA 小程序进行二级结构可视化以及条形图和注释的其他基于 JavaScript 的视图。一个新界面还简化了向 RMDB 提交新化学绘图数据的过程。
