RMDB

A repository of RNA structure probing by chemical or enzymatic mapping

The RNA Mapping Database is an archive that contains results of diverse structural mapping experiments performed on ribonucleic acids. Results submitted to the repository must be manually curated and annotated, ensuring that the data reported is reliable and of high quality. 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.

In the RMDB you can:

Browse or quickly search (top right) the database for a particular RNA of interest.
Mine the data for particular structural or sequence motifs.
Predict the secondary structure of an RNA guided by structure mapping data.
Get started on sharing your data by reviewing the RDAT file format specification.

The RMDB is currently housing 87 entries, for more than 6807 experiments, comprising 4089945 datapoints.

Standardizing chemical footprinting data

This site provides tools and format specifications to make sharing of these experimental data easier and faster.

Want to register?

Play the game!

RNA structure can be fun as well. Join the EteRNA community in the quest for the perfect structure. Your contribution may end up in this database!

Database integration

Please contact us if your lab would like to share RNA structure mapping data through this database.

Useful links

Citation

P Cordero, JB Lucks, R Das, "An RNA Mapping Database for curating RNA structure mapping experiments", 2012, doi: 10.1093/bioinformatics/bts554

RMDB news

May 23, 2013:We have gathered DMS, CMCT, and 1M7 standard-state data for RNA Puzzles 10. RNA Puzzle 10 features two RNAs in complex with one another. Data were gathered for both RNAs in complex and in isolation. The data for RNA #1 is available at RNAPZ10_STD_0001, and the data for RNA #2 is available at RNAPZ10_STD_0002.
May 23, 2013:We have acquired one-dimensional SHAPE, DMS, and CMCT measurements for the ninth RNA puzzle, under a series of analogue ligand conditions. Data is available as entries RNAPZ9_ALG_0001.
May 15, 2013:We have acquired two-dimensional mutate-and-map data (CMCT and nomod) for the eighth RNA Puzzle. Data are available as entries RNAPZ8_CMCT_0001, and RNAPZ8_nomod_0001. We have also acquired one-dimensional HRF (hydroxyl radical footprinting) measurements for the eighth RNA Puzzle. Data is available as entry RNAPZ8_HRF_0001,
May 14, 2013:Data from the EteRNA cloud lab is here! In one shot, we now have expanded our database by more than 5-fold to 4 million data points. And this pipeline will continue, with additional experimental cycles once a month (or more frequently). Check out the EteRNA entries when you browse. And check out EteRNA to join this project in cloud biochemistry!
May 10, 2013:We have acquired two-dimensional mutate-and-map data (CMCT and nomod) for the ninth RNA Puzzle. Data are available as entries RNAPZ9_CMCT_0001, and RNAPZ9_nomod_0001.
May 7, 2013:We have acquired two-dimensional mutate-and-map data (SHAPE and DMS) for the eighth and ninth RNA Puzzle. Data are available as entries RNAPZ8_1M7_0001, RNAPZ8_DMS_0001, RNAPZ9_1M7_0001, and RNAPZ9_DMS_0001.
April 23, 2013:We have acquired one-dimensional SHAPE, DMS, and CMCT measurements for the eighth and ninth RNA puzzle, under no ligand and with ligand conditions. Data are available as entries RNAPZ8_STD_0001, and RNAPZ9_STD_0001,.
April 20, 2013:We have acquired one-dimensional SHAPE, DMS, and CMCT measurements for the seventh RNA puzzle, and two-dimensional mutate-and-map data (SHAPE, DMS, and nomod) as well. Data are available as entries RNAPZ7_STD_0001; RNAPZ7_1M7_0001, RNAPZ7_DMS_0001, and RNAPZ7_nomod_0001.
Oct. 10, 2012:We have acquired one-dimensional SHAPE, DMS, and CMCT measurements for the sixth RNA puzzle, and two-dimensional mutate-and-map data (SHAPE) as well. Data are available as entries RNAPZ6_STD_0001 and RNAPZ6_1M7_0002
Sept. 28, 2012:The paper for the RMDB is out online! Please cite us if you are using the database in your investigations: P Cordero, JB Lucks, and R Das, "An RNA Mapping Database for curating RNA structure mapping experiments", 2012, doi: 10.1093/bioinformatics/bts554

Download all RMDB entries: You can download all entries indexed in the RMDB here