RNALogo

RNALogo generates graphical logos from RNA multiple sequence alignments that integrate primary sequence conservation, consensus secondary structure, and mutual information from base-paired regions.

Key Features:

• Structure-Aware Logo Generation: Produces position-specific letter stacks representing nucleotide conservation within consensus RNA secondary structures.
• Mutual Information Integration: Incorporates mutual information from base-paired positions to capture covariation and structural dependencies.

Scientific Applications:

• RNA Motif and Family Analysis: Supports identification of conserved sequence and structural motifs in regulatory RNAs and comparative analysis across RNA families, including those in Rfam.

Methodology:

RNALogo processes RNA multiple sequence alignments to derive consensus secondary structures and computes nucleotide conservation and base-pair mutual information, rendering these features as integrated structure-based sequence logos.