Output format

DESCRIPTION

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.

EXAMPLE OUTPUT

##gff-version 2 ##source-version NetOGlyc 4.0.0.12 ##date 13-7-15 ##Type Protein #seqname source feature start end score strand frame comment CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 5 5 0.04656 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 11 11 0.0297036 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 15 15 0.296424 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 17 17 0.182807 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 22 22 0.567964 . . #POSITIVE CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 24 24 0.35171 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 26 26 0.558198 . . #POSITIVE CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 27 27 0.182353 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 46 46 0.199041 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 49 49 0.28106 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 56 56 0.0436836 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 61 61 0.0710515 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 70 70 0.107585 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 74 74 0.0440414 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 86 86 0.163292 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 88 88 0.0735873 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 95 95 0.251049 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 99 99 0.335158 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 108 108 0.505881 . . #POSITIVE CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 111 111 0.100125 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 112 112 0.488462 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 115 115 0.314924 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 119 119 0.0818746 . . CSF2_HUMAN netOGlyc-4.0.0.12 CARBOHYD 122 122 0.0480526 . .