IntaRNA - RNA-RNA interaction

IntaRNA predicts interactions between small RNAs (sRNAs) and target mRNAs in bacteria to identify interaction sites and inform sRNA-mediated post-transcriptional regulation.

Key Features:

• Target prediction: Predicts mRNA targets for bacterial sRNAs by analyzing sequence complementarity and thermodynamic stability of RNA-RNA duplexes.
• Interaction domain identification: Maps specific interaction regions within sRNAs and target mRNAs to localize duplex formation sites.
• Regulatory network analysis: Predicts multiple targets per sRNA to facilitate construction of sRNA-mediated regulatory networks.
• Integration with CopraRNA: Incorporates comparative prediction algorithms from CopraRNA to refine target identification and interaction domain mapping.
• Postprocessing functionalities: Performs functional enrichment analysis and provides visualization of interacting regions for interpretation of predicted targets.

Scientific Applications:

• Gene regulation studies: Enables investigation of sRNA-mediated post-transcriptional regulation by predicting sRNA–mRNA interactions.
• Pathway analysis: Uses functional enrichment of predicted targets to identify pathways and biological processes regulated by sRNAs.
• Synthetic biology: Informs design and modification of regulatory circuits by providing sRNA target spectra and interaction site information.

Methodology:

IntaRNA applies sequence alignment and thermodynamic modeling to evaluate the stability of potential RNA-RNA duplexes and can incorporate comparative prediction algorithms from CopraRNA.