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. 2007 Jun 19:8:211.
doi: 10.1186/1471-2105-8-211.

Composition Profiler: a tool for discovery and visualization of amino acid composition differences

Vladimir Vacic  1 , Vladimir N Uversky, A Keith Dunker, Stefano Lonardi
Affiliations

Composition Profiler: a tool for discovery and visualization of amino acid composition differences

Vladimir Vacic et al. BMC Bioinformatics. .

Abstract

Background: Composition Profiler is a web-based tool for semi-automatic discovery of enrichment or depletion of amino acids, either individually or grouped by their physico-chemical or structural properties.

Results: The program takes two samples of amino acids as input: a query sample and a reference sample. The latter provides a suitable background amino acid distribution, and should be chosen according to the nature of the query sample, for example, a standard protein database (e.g. SwissProt, PDB), a representative sample of proteins from the organism under study, or a group of proteins with a contrasting functional annotation. The results of the analysis of amino acid composition differences are summarized in textual and graphical form.

Conclusion: As an exploratory data mining tool, our software can be used to guide feature selection for protein function or structure predictors. For classes of proteins with significant differences in frequencies of amino acids having particular physico-chemical (e.g. hydrophobicity or charge) or structural (e.g. alpha helix propensity) properties, Composition Profiler can be used as a rough, light-weight visual classifier.

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Figures

Figure 1
Figure 1
Composition Profiles of homo- (A) and heterodimerisation (B) interfaces and hub proteins from C. elegans PPI network. Analysis of residues in homo- and heterodimer interfaces against surface residues of monomeric proteins shows slight depletion in hydrophilics (cyan) and enrichement in hydrophobics (black) as a general trend, although homodimer interfaces show closer resemblance to the protein surfaces. Composition profile of hub proteins shows a general enrichment in disorder (red) and depletion in order promoting residues (blue).
Figure 2
Figure 2
Composition profiles of PDB Select 25 (A), surface residues of monomers (B) and DisProt (C) against SwissProt. Plotting the three graphs using the same y-axis scale, same ordering of amino acids and the same color-coding scheme (flexibility) allows for a direct visual comparison between enrichment and depletion patterns in the three datasets.
See this image and copyright information in PMC

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