CorreLogo

CorreLogo generates three-dimensional sequence logos from RNA and DNA multiple sequence alignments to visualize per-column information content, residue composition, pairwise mutual information, and gap fractions for detection of correlated nucleotide positions.

Key Features:

• 3D Sequence Logo Representation: Represents alignments in three dimensions where the first two dimensions encode information content and residue composition and the third dimension encodes mutual information between column pairs.
• Single-Column Visualization: Visualizes each alignment column as color-coded 3D bars labeled with nucleotide letters to show position-specific residue composition.
• Mutual Information Calculation: Computes and displays mutual information between pairs of alignment positions to indicate correlated residues.
• Gap Fraction Visualization: Reports and visualizes position-specific gap fractions within the alignment.
• Output Formats: Exports visualizations in VRML and JVX file formats.

Scientific Applications:

• Structural analysis of RNA and DNA: Aids identification of correlated nucleotide positions that may indicate structural or functional interactions in RNA and DNA alignments.
• tRNA Analysis: Reveals correlations within tRNA structures, including relationships involving the anticodon region and the amino acid acceptor stem.
• Base Pair Identification: Assists identification of potential base pairs by combining nucleotide composition and mutual information signals.

Methodology:

Analyzes user-submitted alignments by calculating information content, residue composition, mutual information, and gap fractions, then maps these metrics onto a three-dimensional visual representation using color-coded bars and nucleotide labels.