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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	.	.	





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