RILogo

RILogo generates RNA–RNA interaction logos from structure-annotated sequence pairs or multiple sequence alignments. It visualizes base pairing patterns and quantifies conserved interactions using mutual information metrics that incorporate evolutionary distance.

Key Features:

• RNA–RNA Interaction Logo Visualization: Produces graphical logos representing base pairing patterns from single sequences or homologous alignments.
• Alignment-Based Mutual Information Analysis: Computes mutual information for base-paired columns to identify conserved interaction sites.
• Evolution-Aware Mutual Information Metrics: Implements two novel mutual information measures that weight covariance by evolutionary distance to improve detection accuracy.
• Flexible Input Support: Accepts structure-annotated RNA sequence pairs and multiple sequence alignments.

Scientific Applications:

• Non-Coding RNA Interaction and Evolution Studies: Enables identification and comparative analysis of conserved RNA interaction motifs across species.

Methodology:

RILogo analyzes structure-annotated RNA sequences or alignments to compute mutual information between base-paired positions, applies evolutionary distance-weighted metrics to refine covariance signals, and renders interaction logos to represent conserved RNA–RNA base pairing patterns.