Riboswitches are cis-regulatory conserved non-coding structural RNA sensors that are present in the 5' untranslated regions (UTRs) of the bacterial mRNA, bind to specific ligands and control the expression of downstream genes. RiboD is a database of prokaryotic riboswitches that provides a comprehensive list of computationally predicted riboswitches, riboswitch regulated genes and operons from the sequenced prokaryotic genomes available in the RefSeq. Currently, the RiboD database contains riboswitches for 1777 prokaryotic genomes and covers 31 metabolite and ion sensing riboswitch classes. The database supports a number of search capabilities to facilitate easy access to and utilization of the information associated with riboswitches as per user needs. Users can search for riboswitches based on riboswitch class, riboswitch-regulated genes, annotated biological processes/pathways of riboswitch-regulated genes and phylum. All of the listed computationally identified tandem riboswitches can be found by selecting the “Tandem Riboswitches” option under the search tab. In the advanced search option, the user can specify multiple fields to refine the search query and extract the specific information. The user can download the required information generated from each search query in excel file format. RiboD is the first database of prokaryotic riboswitches which provides a very useful resource for researchers can be utilized for the better understanding and further exploration of the riboswitch-based gene regulations in bacteria and archaea.
If you make use of the data presented here, please cite the following article
• Mukherjee, S., Mandal, S.D., Gupta, N., Retwitzer, M.D., Barash, D., and Sengupta, S. (2019) "RiboD: A comprehensive database for prokaryotic riboswitches", Bioinformatics, btz093