NetOGlyc protocols

View NetOGlyc computational protocol

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NetOGlyc specifications

Information


Unique identifier OMICS_02441
Name NetOGlyc
Interface Web user interface, Application programming interface
Restrictions to use None
Input data A set of sequences.
Input format FASTA
Computer skills Basic
Version 4.0
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Documentation


Maintainer


  • person_outline Hiren Joshi <>

Additional information


Access to a standalone version available upon request.

Information


Unique identifier OMICS_02441
Name NetOGlyc
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A single sequence (just the amino acids) or a number of sequences.
Input format FASTA
Output data A list of potential glycosylation sites, showing their positions in the sequence and the prediction confidence scores.
Operating system Unix/Linux
Computer skills Advanced
Version 4.0
Stability Stable
Requirements
DisEMBL, NetSurfP, TMHMM

Taxon


  • Primates
    • Homo sapiens

Versioning


Add your version

Documentation


Maintainer


This tool is not maintained anymore.

Additional information


Access to a standalone version available upon request.

Publications for NetOGlyc

NetOGlyc in pipeline

2015
PMCID: 4307335
PMID: 25594872
DOI: 10.3390/ijms16011806

[…] for signal peptide sequence prediction. prosite program of expasy (http://www.expasy.org/cgi-bin/prosite/scanview.cgi?scanfile=294556012219.scan.gz) was used for sp1 protein domains analyses. cbs netoglyc 3.1 was used for glycosylation sites prediction (http://www.cbs.dtu.dk/services/netoglyc/). cbs netphos 2.0 was used for phosphorylation sites prediction […]


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NetOGlyc in publications

 (301)
PMCID: 5919079
PMID: 29694383
DOI: 10.1371/journal.pone.0193525

[…] and o-linked amino acid glycosylation in the 2nd hvr of g protein gene of study sequences (n = 28) was predicted by the netnglyc 1.0 (http://www.cbs.dtu.dk/services/netnglyc/) server and the netoglyc 4.0 server (http://www.cbs.dtu.dk/services/netoglyc/) respectively ().the potential n-linked glycosylation sites were defined as asn-xaa-ser/thr (where xaa is not proline). further, […]

PMCID: 5910400
PMID: 29679010
DOI: 10.1038/s41598-018-24568-9

[…] tree which was exported to figtree (version 1.4.2, http://tree.bio.ed.ac.uk/software/figtree/). glycosylation sites were predicted using netnglyc1.0 (http://www.cbs.dtu.dk/services/netnglyc/) and netoglyc4.0 (http://www.cbs.dtu.dk/services/netoglyc/). molecular weight and isoelectric point (pi) of proteins were calculated at expasy(http://web.expasy.org/compute_pi/). we used muscle […]

PMCID: 5917092
PMID: 29725590
DOI: 10.3389/fchem.2018.00128

[…] modifications. indeed, 1 asn-xaa-ser/thr sequon and 44 ser-thr residues were predicted in ttcbh6 sequence by using the netnglyc 1.0 server (http://www.cbs.dtu.dk/services/netnglyc/) and the netoglyc 3.1 server (http://www.cbs.dtu.dk/services/netoglyc/), while 1 asn-xaa-ser/thr sequon and 23 ser-thr residues were predicted in ttcbh7 sequence., the purified ttcbh6 and ttcbh7 were assayed […]

PMCID: 5936059
PMID: 29685999
DOI: 10.1242/bio.030361

[…] which indicates that also the 170 kda prc species holds a limited number of o-linked glycans. of note, in silico analysis predicts 231 o-glycosylation sites within the prc primary sequence (netoglyc 4.0, http://www.cbs.dtu.dk/services/netoglyc). the considerable discrepancy between the predicted molecular mass of prc (163.5 kda) and the apparent mass of the fully glycosylated protein […]

PMCID: 5903068
PMID: 29692765
DOI: 10.3389/fmicb.2018.00693

[…] v. 1.1 platform was used to predict subcellular location. hydrophobic domains were predicted by the tmhmm 2.0 server. potential sites of n- and o-glycosylation were identified by netnglyc 1.0 and netoglyc 4.0, respectively. interproscan v. 4.8 software was used to identify different protein domains. prediction of gpi-anchoring sites was performed with the predgpi program., the open reading […]


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NetOGlyc institution(s)
Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen, Denmark; Center for Biological Sequence Analysis, Department of Systems Biology Technical University of Denmark, Lyngby, Denmark; IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Horsholm, Denmark; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
NetOGlyc funding source(s)
Supported by Kirsten og Freddy Johansen Fonden, A.P. Moller og Hustru Chastine Mc-Kinney Mollers Fond til Almene Formaal, The Carlsberg Foundation, The Novo Nordisk Foundation, The Danish Research Councils, a programme of excellence from the University of Copenhagen, the Sino-Danish Breast Cancer Centre and The Danish National Research Foundation (DNRF107).

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