Composition Profiler

Composition Profiler detects enrichment and depletion patterns in amino acid composition by comparing a query sample against a reference sample to reveal associations with physico-chemical and structural properties.

Key Features:

• Input Flexibility: Requires two samples (query and reference), where the reference can be SwissProt, PDB, representative proteins from the organism, or proteins with contrasting functional annotations.
• Semi-automatic discovery: Enables semi-automatic identification of enrichment or depletion patterns in amino acids.
• Composition comparison analysis: Assesses differences in amino acid composition between query and reference to identify significant variations in amino acid frequencies that may correlate with protein function or structure.
• Grouping by properties: Analyzes amino acids individually or grouped by physico-chemical properties (e.g., hydrophobicity, charge) or structural properties (e.g., alpha helix propensity).
• Output formats: Presents results in textual and graphical formats.
• Exploratory feature selection: Supports exploratory data mining to guide feature selection for developing predictors of protein function or structure.
• Visual classification: Provides a rough visual classifier for protein classes exhibiting notable differences in amino acid composition.

Scientific Applications:

• Protein function inference: Identify compositional signatures that correlate with specific protein functions to support functional annotation.
• Structural characterization: Detect amino acid enrichment or depletion linked to structural properties such as secondary-structure propensities.
• Predictor development: Inform feature selection for machine-learning models predicting protein function or structural classes.
• Evolution and adaptation studies: Explore hypotheses about protein evolution, adaptation, or functional specialization based on amino acid composition differences.

Methodology:

Compare query and reference amino acid frequency distributions to identify statistically significant enrichment or depletion, analyzing residues individually or grouped by physico-chemical and structural properties.