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Bioinformatics Advance Access published online on February 2, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti299
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Bioinformatics © Oxford University Press 2005; all rights reserved.
Received September 29, 2004
Revised January 25, 2005
Accepted January 27, 2005

Article

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

Niklaus Fankhauser 1 and Pascal Mäser 1*

1 Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland

* To whom correspondence should be addressed.
Pascal Mäser, E-mail: pascal.maeser{at}izb.unibe.ch


  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.

Supplementary Information: Positive training set, performance test sets, and lists of predicted GPI-anchored proteins from different eukaryotes in fasta format.


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