Prokaryotic genome analysis pipeline based on Riboswitch Scanner for detecting riboswitches and riboswitch-regulated genes from complete genome sequences. To use this application for your genome of interest, (i) Upload nucleotide sequence in NCBI fna file format & genomic feature in NCBI gff file format (ii) Choose from the the riboswitch classes and (iii) Click on the Scan button.

Note: For detecting riboswitches in partial genome sequences and/or if you do not have the genomic feature file in gff format, use the Riboswitch Scanner.

Upload complete genome Sequence File in NCBI fna file format (FASTA)
Upload genomic feature file in NCBI gff file format

Choose from the following riboswitch families you want to search:

AdoCbl Cobalamin c-di-GMP-I c-di-GMP-II
Fluoride FMN glmS Glutamine
Glycine Lysine Mg_sensor MOCO_RNA_motif
NiCo PreQ1 preQ1-II purine
SAM/SAM-I SAM-alpha/SAM-II SAM-IV SAH_riboswitch
SAM-SAH SMK_box_riboswitch THF TPP
ydaO-yuaA (cyclic di-AMP) ykkC-yxkD (Guanidine-I) mini-ykkC (Guanidine-II) ykkC-III (Guanidine-III)
ykoK (Mg2+) yybP-ykoY (Mn2+) ZMP-ZTP


If you use this Riboswitch Scanner based application in your research, please cite our 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.