WebLogo 3

WebLogo 3 generates sequence logos that represent position-specific residue conservation and variability from multiple sequence alignments using information-theoretic measures.

Key Features:

• Stacked-letter logos: Creates a stack of letters at each alignment position to display position-specific composition.
• Information content in bits: Quantifies conservation per position in bits derived from information theory to reflect variability or conservation.
• Residue representation: Uses symbols for amino acids or nucleotides with individual heights proportional to their relative frequencies at each position.
• Quantitative depiction: Provides a more detailed and quantitative depiction of sequence similarity than traditional consensus sequences.
• Configurable visualization parameters: Offers options to tailor logo appearance and metrics for specific analytical needs.

Scientific Applications:

• Motif visualization: Visualizes conserved motifs in protein or nucleic acid sequences from multiple sequence alignments.
• Functional inference: Aids identification of functional domains and binding sites by highlighting conserved residues.
• Evolutionary analysis: Assesses sequence variability and conservation to inform evolutionary relationships and selective pressures.

Methodology:

For each column of a multiple sequence alignment, compute information content in bits and construct stacks of letters whose heights are proportional to residue relative frequencies.