Prediction of putative riboswitches in Genomic Datasets

Riboswitches are cis-regulatory segments of the genome that control gene expression of adjacent genes by undergoing conformational changes on ligand binding. Riboswitches are categorized into different classes according to the type of ligand that binds to it.

The web-application Riboswitch Scanner has been developed to detect riboswitches from genomic sequences with high sensitivity and specificity. The tool uses a method based on profile Hidden Markov Models (pHMMs) for detecting riboswitches. Riboswitch Scanner also provides the putative locations of the riboswitches in the genomic sequences. The Riboswitch Scanner web-application can be accessed from the 'Scanner' tab of this webpage. The current version of Riboswitch Scanner is able to detect 24 classes of riboswitches from complete genome sequences as well as from partial genome sequences. For sequences containing potential riboswitches belonging to new riboswitch classes that are not listed, the user can select the 'Other' option under the riboswitch family section and upload a FASTA file containing at least four seed sequences of the new (user-specified) family to search for instances of those riboswitches.

When riboswitches are detected either in main or complementary strand, the output provides the pHMM score, E-value and start and end positions of the corresponding riboswitch sequence in the genome. The minimum free-energy structure, for each detected riboswitch, in dot-bracket notation can also be viewed via a link provided in the output page. The secondary structure of each riboswitch obtained using the RNAfold package along with the consensus secondary structure of the corresponding riboswitch family courtesy of Rfam can also be downloaded.

If you use Riboswitch Scanner in your research, please cite the following publications:

(1) Mukherjee, S. and Sengupta, S. (2016) "Riboswitch Scanner: An efficient pHMM-based web-server to detect riboswitches in genomic sequences", Bioinformatics, 32 (5): 776-778.

(2) Singh, P., et al. (2009) "Riboswitch detection using profile hidden Markov models", BMC bioinformatics 10 (1): 325.