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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


No version available

Documentation


Maintainer


This tool is not maintained anymore.

Additional information


Access to a standalone version available upon request.

Publications for NetOGlyc

NetOGlyc citations

 (113)
library_books

Genetically engineered two warhead evasins provide a method to achieve precision targeting of disease relevant chemokine subsets

2018
Sci Rep
PMCID: 5910400
PMID: 29679010
DOI: 10.1038/s41598-018-24568-9

[…] tic 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 in Megalign […]

library_books

A Carbohydrate Moiety of Secreted Stage Specific Glycoprotein 4 Participates in Host Cell Invasion by Trypanosoma cruzi Extracellular Amastigotes

2018
Front Microbiol
PMCID: 5903068
PMID: 29692765
DOI: 10.3389/fmicb.2018.00693

[…] etP 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. […]

library_books

Lipophosphoglycan 3 From Leishmania infantum chagasi Binds Heparin With Micromolar Affinity

2018
Bioinform Biol Insights
PMCID: 5858678
PMID: 29568220
DOI: 10.1177/1177932218763363

[…] lycosylphosphatidylinositol (GPI)-anchor regions was assessed using GPI-SOM 1.5, big-PI Predictor, and PredGPI-GPI. To predict regions with N- and O-linked glycosylation, we used the NetNGlyc 1.0 and NetOGlyc 4.0 servers, respectively. The search for domains was performed using Pfam 30.0 database. The multiple alignment of the LPG3 amino acid sequence for the species L infantum chagasi (LinJ.29.07 […]

library_books

Identification, characterization and heparin binding capacity of a spore wall, virulence protein from the shrimp microsporidian, Enterocytozoon hepatopenaei (EHP)

2018
PMCID: 5848443
PMID: 29530076
DOI: 10.1186/s13071-018-2758-z

[…] m/current_release/Pfam-A.seed.gz. Phosphorylation site prediction was carried out by SCANPROSITE tool (http://prosite.expasy.org/prosite.html). NETNGLYC (http://www.cbs.dtu.dk/services/NetNGlyc/) and NETOGLYC (http://www.cbs.dtu.dk/services/NetOGlyc/) were used to predict N- and O-glycosylation sites, respectively. […]

library_books

The N terminal domain of a tick evasin is critical for chemokine binding and neutralization and confers specific binding activity to other evasins

2018
PMCID: 5912465
PMID: 29487134
DOI: 10.1074/jbc.RA117.000487

[…] was plotted using the EMBOSS () program, Plotcon (http://www.bioinformatics.nl/emboss-explorer/).7 Glycosylation sites were predicted using NetNGlyc1.0 (http://www.cbs.dtu.dk/services/NetNGlyc/) and NetOGlyc4.0 (http://www.cbs.dtu.dk/services/NetOGlyc/) ().7 The molecular weight and pI of proteins were calculated at ExPASy (http://web.expasy.org/compute_pi/).7 We performed homology modeling using […]

library_books

Analysis of Homologs of Cry toxin Receptor Related Proteins in the Midgut of a Non Bt Target, Nilaparvata lugens (Stål) (Hemiptera: Delphacidae)

2018
PMCID: 5804751
PMID: 29415259
DOI: 10.1093/jisesa/iex102

[…] P 4.1 (). GPI-anchor signal at the C-terminus was predicted using PredGPI, FragAnchor, and big-PI Predictor. N-glycosylation and O-glycosylation sites were predicted by the NetNglyc 1.0 Server () and NetOglyc 4.0 Server (), respectively. Transmembrane helices of each protein were predicted by the TMHMM 2.0 Server (http://www.cbs.dtu.dk/services/TMHMM/). […]

Citations

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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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