Skip Navigation


Bioinformatics Advance Access originally published online on February 2, 2005
Bioinformatics 2005 21(9):1846-1852; doi:10.1093/bioinformatics/bti299
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/9/1846    most recent
bti299v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (15)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Fankhauser, N.
Right arrow Articles by Mäser, P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Fankhauser, N.
Right arrow Articles by Mäser, P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

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

Niklaus Fankhauser and Pascal Mäser *

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

*To whom correspondence should be addressed.

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{at}izb.unibe.ch

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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Protein Eng Des SelHome page
J. Ren, L. Wen, X. Gao, C. Jin, Y. Xue, and X. Yao
CSS-Palm 2.0: an updated software for palmitoylation sites prediction
Protein Eng. Des. Sel., August 27, 2008; (2008) gzn039v1.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. C. Doxey, M. W. F. Yaish, B. A. Moffatt, M. Griffith, and B. J. McConkey
Functional Divergence in the Arabidopsis {beta}-1,3-Glucanase Gene Family Inferred by Phylogenetic Reconstruction of Expression States
Mol. Biol. Evol., April 1, 2007; 24(4): 1045 - 1055.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
E. J. Tarcha, V. Basrur, C.-Y. Hung, M. J. Gardner, and G. T. Cole
Multivalent Recombinant Protein Vaccine against Coccidioidomycosis.
Infect. Immun., October 1, 2006; 74(10): 5802 - 5813.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
P. R. Gilson, T. Nebl, D. Vukcevic, R. L. Moritz, T. Sargeant, T. P. Speed, L. Schofield, and B. S. Crabb
Identification and Stoichiometry of Glycosylphosphatidylinositol-anchored Membrane Proteins of the Human Malaria Parasite Plasmodium falciparum
Mol. Cell. Proteomics, July 1, 2006; 5(7): 1286 - 1299.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
E. J. Tarcha, V. Basrur, C.-Y. Hung, M. J. Gardner, and G. T. Cole
A Recombinant Aspartyl Protease of Coccidioides posadasii Induces Protection against Pulmonary Coccidioidomycosis in Mice
Infect. Immun., January 1, 2006; 74(1): 516 - 527.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.