Database Commons

a catalog of worldwide biological databases

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.

SUMMARY: We have established an RNA mapping database (RMDB) to enable structural, thermodynamic and kinetic comparisons across single-nucleotide-resolution RNA structure mapping experiments. The volume of structure mapping data has greatly increased since the development of high-throughput sequencing techniques, accelerated software pipelines and large-scale mutagenesis. For scientists wishing to infer relationships between RNA sequence/structure and these mapping data, there is a need for a database that is curated, tagged with error estimates and interfaced with tools for sharing, visualization, search and meta-analysis. Through its on-line front-end, the RMDB allows users to explore single-nucleotide-resolution mapping 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 53 entries, describing more than 2848 experiments of 1098 RNA constructs in several solution conditions and is growing rapidly.
AVAILABILITY: Freely available on the web at http://rmdb.stanford.edu.
CONTACT: rhiju@stanford.edu.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.