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Inferring sub-cellular localization through automated lexical analysis.

Rajesh Nair1, Burkhard Rost

  • 1CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA. nair@cubic.bioc.coplumbia.edu

Bioinformatics (Oxford, England)
|August 10, 2002
PubMed
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LOCkey is a new automated method that analyzes protein keywords to predict sub-cellular localization. This tool achieved over 82% accuracy, identifying thousands of new localization annotations for key eukaryotic proteomes.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Proteomics

Background:

  • SWISS-PROT database contains protein functional keywords but limited sub-cellular localization data.
  • Protein function keywords can infer sub-cellular localization, a task traditionally done by experts.
  • Automated methods are needed to keep pace with the growing volume of sequence data.

Purpose of the Study:

  • To develop a fully automated method for predicting protein sub-cellular localization using SWISS-PROT keywords.
  • To supplement existing functional information with predicted localization data.
  • To address the gap in biochemical characterization of rapidly growing sequence data.

Main Methods:

  • Developed LOCkey, a lexical analysis tool for SWISS-PROT keywords.

Related Experiment Videos

  • Employed a fully automated approach for keyword analysis and localization assignment.
  • Utilized full cross-validation for method accuracy assessment.

    • Main Results:

    • LOCkey achieved over 82% accuracy in cross-validation tests.
    • Identified sub-cellular localization for fewer than half of SWISS-PROT proteins due to annotation limitations.
    • Annotated approximately 8000 new sub-cellular localizations across five eukaryotic proteomes (yeast, worm, fly, plant, human subset).

    Conclusions:

    • LOCkey provides a valuable automated tool for predicting protein sub-cellular localization.
    • The method successfully identified a significant number of novel localization annotations.
    • LOCkey can aid in the biochemical characterization of proteomes, complementing existing functional data.