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


BACKGROUND
GPI-SOM is accessible on-line at http://gpi.unibe.ch. The source code (written in C) is available on the same website.


BACKGROUND
Positive training set, performance test sets and lists of predicted GPI-anchored proteins from different eukaryotes in fasta format.
Fankhauser
Niklaus
N
Institute of Cell Biology, University of Bern, Switzerland.
Mäser
Pascal
P
D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D002462:Cell Membrane / Q000737:chemistry* / Q000378:metabolism; D017261:Glycosylphosphatidylinositols / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology; D012984:Software; D013045:Species Specificity
D017261:Glycosylphosphatidylinositols; D008565:Membrane Proteins