Identification of GPI anchor attachment signals by a Kohonen self-organizing map

  • Authors:

  • Niklaus Fankhauser;Pascal Mäser

  • Affiliations:

  • Institute of Cell Biology, University of Bern CH-3012 Bern, Switzerland;Institute of Cell Biology, University of Bern CH-3012 Bern, Switzerland

  • Venue:
  • Bioinformatics
  • Year:
  • 2005

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Abstract

Motivation: Anchoring of proteins to the extracytosolic leaflet of membranes via C-terminal attachment of glycosylphosphatidylinositol (GPI) is ubiquitous and essential in eukaryotes. The signal for GPI-anchoring is confined to the C-terminus of the target protein. In order to identify anchoring signals in silico, we have trained neural networks on known GPI-anchored proteins, systematically optimizing input parameters. Results: A Kohonen self-organizing map, GPI-SOM, was developed that predicts GPI-anchored proteins with high accuracy. In combination with SignalP, GPI-SOM was used in genome-wide surveys for GPI-anchored proteins in diverse eukaryotes. Apart from specialized parasites, a general trend towards higher percentages of GPI-anchored proteins in larger proteomes was observed. Availability: GPI-SOM is accessible on-line at http://gpi.unibe.ch. The source code (written in C) is available on the same website. Contact: pascal.maeser@izb.unibe.ch Supplementary information: Positive training set, performance test sets and lists of predicted GPI-anchored proteins from different eukaryotes in fasta format.