Riboswitch Scanner

Riboswitch Scanner identifies riboswitches in partial and complete genomic sequences by using profile Hidden Markov Models (pHMMs) to detect metabolite-binding noncoding RNAs located in 5' untranslated regions (5' UTRs).

Key Features:

• Automated Pipeline: Provides an automated computational pipeline for scanning genomic sequences and reporting candidate riboswitch loci.
• pHMM-Based Detection: Employs profile Hidden Markov Models (pHMMs) tailored to recognize specific riboswitch classes based on sequence conservation and binding properties.
• High Sensitivity and Specificity: Optimized for high sensitivity and specificity in identifying riboswitch elements across diverse genomic datasets.

Scientific Applications:

• Gene regulation studies: Identifying metabolite-responsive riboswitches in 5' UTRs to elucidate RNA-mediated regulation of gene expression.
• Metabolic control analysis: Linking detected metabolite-binding riboswitches to changes in gene expression in response to cellular metabolite levels.
• Microbial genetics: Annotating riboswitches in microbial genomes to investigate regulatory networks and operon structures.
• Synthetic biology: Discovering natural riboswitch sequences and classes that can be repurposed as regulatory parts.
• Drug discovery: Characterizing riboswitch classes and ligand-binding motifs that are potential targets for small-molecule intervention.

Methodology:

Uses profile Hidden Markov Models (pHMMs) tailored to specific riboswitch classes to scan partial and complete genomic sequences and identify candidate metabolite-binding noncoding RNAs in 5' UTRs.