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

Vladimir Vacic, Vladimir N. Uversky, A. Keith Dunker, Stefano Lonardi

Research output: Contribution to journalArticle

201 Citations (Scopus)

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. α helix propensity) properties, Composition Profiler can be used as a rough, light-weight visual classifier.

Original languageEnglish (US)
Article number211
JournalBMC bioinformatics
Volume8
DOIs
StatePublished - Jun 19 2007

Fingerprint

Amino Acids
Amino acids
Visualization
Proteins
Protein
Chemical analysis
Protein Databases
Query
Hydrophobicity
Data Mining
Depletion
Helix
Software Tools
Hydrophobic and Hydrophilic Interactions
Structural Properties
Web-based
Feature Selection
Chemical properties
Rough
Data mining

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

Composition Profiler : A tool for discovery and visualization of amino acid composition differences. / Vacic, Vladimir; Uversky, Vladimir N.; Dunker, A. Keith; Lonardi, Stefano.

In: BMC bioinformatics, Vol. 8, 211, 19.06.2007.

Research output: Contribution to journalArticle

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