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NetOGlyc 2.0 prediction server Introduction Although technically this is not a software package you can download and use yourself, the NetOGlyc 2.0 server is a valuable research tool and thus worthy to mention here. The NetOGlyc 2.0 WWW server is a prediction server of mucin type O-glycosylation sites in mammalian proteins. Upon submission of a protein sequence, it uses a neural network approach to predict the sites, and output is in the form of a table and a graph. Background information The specificities of the UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase family which links the carbohydrate GalNAc to the side chain of certain serine and threonine residues in mucin type glycoproteins are presently unknown. The specificity seems to be modulated by sequence context, secondary structure and surface accessibility. The sequence context of glycosylated threonines was found to differ from that of serine, and the sites were found to cluster. Non-clustered sites had a sequence context different from that of clustered sites. Charged residues were disfavoured at position -1 and +3. A jury of artificial neural networks was trained to recognize the sequence context and surface accessibility of 299 known and verified mucin type O-glycosylation sites extracted from O-GLYCBASE. The cross-validated NetOglyc network system correctly found 83% of the glycosylated and 90% of the non-glycosylated serine and threonine residues in independent test sets, thus proving more accurate than matrix statistics and vector projection methods. Information supplied by: Jan Hanssen Resources and further information
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Direct questions or comments to Bioinformer Editor. This page last modified Friday, 16 July, 1999. (c) 1997-1999 EMBL-EBI. All Rights Reserved. |