CopraRNA web server

CopraRNA predicts bacterial small RNA (sRNA) targets and interaction domains by integrating comparative genomic information and leveraging IntaRNA-based interaction scoring to improve regulatory network inference.

Key Features:

• Comparative genomic integration: Integrates comparative genomic information across multiple bacterial genomes to refine sRNA target predictions.
• IntaRNA-based prediction: Leverages IntaRNA interaction scoring as the basis for predicting sRNA–mRNA interactions.
• sRNA target and interaction domain prediction: Predicts specific mRNA targets and corresponding sRNA–mRNA interaction regions (interaction domains).
• Functional enrichment analysis: Performs functional enrichment analysis on predicted target sets to identify overrepresented functions or pathways.
• Interaction-region visualization: Produces visual representations of interacting regions between sRNAs and mRNAs.
• Extension of Freiburg RNA Tools: Implements its prediction and postprocessing functionality as an extension of the Freiburg RNA Tools platform.
• Postprocessing for interpretability: Provides postprocessing steps to enhance interpretation of predicted interactions.
• Comparative approach increases reliability: Uses cross-species comparative evidence to increase the reliability of predictions relative to single-genome methods.

Scientific Applications:

• Regulatory network inference: Identifies sRNA–mRNA interactions to support reconstruction of bacterial regulatory networks.
• Gene regulation studies: Maps interaction domains to elucidate mechanisms of sRNA-mediated regulation of gene expression.
• Microbial physiology research: Links predicted sRNA targets and enriched functions to physiological processes in bacteria.

Methodology:

Integrates comparative genomic data, uses IntaRNA-based interaction prediction to predict sRNA targets and interaction domains, and applies functional enrichment analysis and interaction-region visualization as postprocessing steps.