The Stanford RNA Mapping Database for sharing and visualizing RNA structure mapping experiments

TL;DR

The Stanford RNA Mapping Database (RMDB) provides a comprehensive platform for sharing, visualizing, and analyzing high-throughput RNA structure mapping data, facilitating advanced RNA research.

Contribution

This paper introduces the RMDB, a new database that enables sharing, visualization, and meta-analysis of large-scale RNA structure mapping data from high-throughput experiments.

Findings

Contains 38 entries with 2659 RNA sequences

Houses 355,084 data points for RNA structure mapping

Supports various visualization and data download formats

Abstract

We have established an RNA Mapping Database (RMDB) to enable a new generation of structural, thermodynamic, and kinetic studies from quantitative single-nucleotide-resolution RNA structure mapping (freely available at http://rmdb.stanford.edu). Chemical and enzymatic mapping is a rapid, robust, and widespread approach to RNA characterization. Since its recent coupling with high-throughput sequencing techniques, accelerated software pipelines, and large-scale mutagenesis, the volume of mapping data has greatly increased, and there is a critical need for a database to enable sharing, visualization, and meta-analyses of these data. Through its on-line front-end, the RMDB allows users to explore single-nucleotide-resolution chemical accessibility data in heat-map, bar-graph, and colored secondary structure graphics; to leverage these data to generate secondary structure hypotheses; and to download the data in standardized and computer-friendly files, including the RDAT and community-consensus SNRNASM formats. At the time of writing, the database houses 38 entries, describing 2659 RNA sequences and comprising 355,084 data points, and is growing rapidly.