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The RNA Mapping Database is an archive that contains results of diverse structural mapping experiments performed on ribonucleic acids. Results submitted to the repository are manually curated and annotated, ensuring reliability and quality of reported data. With a total of datapoints , RMDB currently houses entries, describing more than experiemnts of RNA constructs in several solution conditions and has been growing rapidly .
In addition, RMDB contributes greatly to the EteRNA videogame/synthetic biology project, and the RNA Puzzles blind RNA structure prediction challenges. It will continue to benefit data sharing for RNA structue mapping community.
The ultimate goal of the RMDB is to provide a centralized, curated, data-sharing platform with visualization and structure prediction tools for rapid analysis and meta-analysis of these data.
Chemical mapping data entries from Das lab in-house and published experiments.
Availability of such data enables critical review and discussion on previous interpretations, as well as demand for improved experimental and computational techniques.
RNA Puzzles a collective experiment for blind RNA structure prediction, with a goal to assess the cutting edge of RNA structure prediction techniques.
A dozen of challenge rounds has encouraged the RNA structure prediction community in their efforts to improve models, techiques and tools for automatic RNA three-dimensional structure prediction.
EteRNA is a game where players become citizen scientists, working together to better understand and predict the behavior of RNA.
Wet laboratory data of dozens of cycles of designs by enthusiasts are deposited, mined, and distilled into new rules that significantly outperform prior algorithms in experimental accuracy of RNA structure designs.
RNA Data (RDAT) text file format is an annotation-based specification for RNA structure mapping experiments that is both computer friendly and can be easily read by humans. The RMDB database schema closely follows the organization of RDAT files, making it easier to manage and expose each entry’s data.
We have tools and guidance available for data preparation, format validation, and data submission. Data will be reviewed and approved by RMDB team before public release.
RMDB allows advanced search for particular structural or sequence motifs of interest. Fast and efficient filtering and retrieval of data facilitates in-depth data and feature mining.
Archive of entire database (all RMDB entries) are available for further processing locally.
RMDB Web API enables retrieval of entire or particular datasets in JSON format.
Structural Server provides facility for RNA secondary structure predictions using chemical mapping data.
RDAT format bonus and RMDB entries are supported as input. Non-parametric bootstrapping reports confidence estimate of helices.
RMDB provides tools that can be used for the analysis of electropherograms in the context of RNA structure mapping.
RDATKit and HiTRACE are freely downloadable, as well as accessible Primerize server. MAPseeker is freely available for non-commercial use. For other tools, please contact us.