WebLogo

WebLogo generates sequence logos that graphically summarize positional conservation and variability in multiple sequence alignments by representing amino acids or nucleic acids.

Key Features:

• Graphical Representation: Each sequence logo comprises vertically stacked letters at each alignment position, with total stack height quantified in bits to indicate the degree of conservation.
• Symbol Height and Frequency: Individual symbol heights within each stack reflect the relative frequency of each amino acid or nucleic acid at that position.
• Customization Options: Provides options to adjust logo generation parameters and output settings to tailor analyses and visual representation.

Scientific Applications:

• Conservation Analysis: Quantifies and visualizes position-specific conservation across multiple sequence alignments using information-theoretic measures.
• Motif Identification: Facilitates rapid identification of sequence motifs and position-specific preferences within alignments.
• Functional and Evolutionary Inference: Aids interpretation of molecular function and evolutionary relationships by highlighting conserved and variable positions.

Methodology:

Analyzes multiple sequence alignments, quantifies conservation at each position using information theory (measured in bits), and represents the results as sequence logos composed of stacked symbols.