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

Bioinformatics. 2005 May 1;21(9):1846-52. doi: 10.1093/bioinformatics/bti299. Epub 2005 Feb 2.


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 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Animals
  • Binding Sites
  • Cell Membrane / chemistry*
  • Cell Membrane / metabolism
  • Glycosylphosphatidylinositols / chemistry*
  • Glycosylphosphatidylinositols / metabolism
  • Humans
  • Membrane Proteins / chemistry*
  • Membrane Proteins / metabolism
  • Protein Binding
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*
  • Signal Transduction / physiology
  • Software*
  • Species Specificity


  • Glycosylphosphatidylinositols
  • Membrane Proteins