The output conforms to the
GFF version 2
format.
For each input sequence the server prints a list of potential glycosylation
sites, showing their positions in the sequence and the prediction confidence
scores. Only the sites with scores higher than
0.5
are predicted as glycosylated and marked with the string "#POSITIVE" in the
comment field.
The example below shows the output for human granulocyte-macrophage
colony-stimulating factor,
The example below shows the output for human granulocyte-macrophage
colony-stimulating factor, taken from the
UniProt
entry
CSF2_HUMAN.
Currently, 4 sites have been experimentally annotated for this protein, and
NetOGlyc predicts that two of these are glycosylated. Additionally, it predicts
an additional site is glycosylated at site 108. Occupancy of O-glycosylation
sites can vary in-vivo depending on the cells that are expressing the protein.
The interactions between sites of initial O-Glycosylation with subsequent sites
of glycosylation are yet to be fully elucidated, while our capability to
precisely predict the substrate specificity of individual GalNAc-Ts remains
limited. The combination of these factors mean that although NetOGlyc will
attempt to predict individual sites of glycosylation, a safe interpretation of
a positive prediction is that the protein in that local region is more likely
to carry O-GalNAc modifications.