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Bioinformatics. 2005 May 1;21(9):1846-52. Epub 2005 Feb 2.

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

Author information

1
Institute of Cell Biology, University of Bern, Switzerland.

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.

PMID:
15691858
DOI:
10.1093/bioinformatics/bti299
[Indexed for MEDLINE]

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