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NetNGlyc specifications

Information


Unique identifier OMICS_02442
Name NetNGlyc
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Documentation


Maintainer


  • person_outline Ramneek Gupta

Additional information


Access to a standalone version available upon request. http://www.cbs.dtu.dk/cgi-bin/nph-runsafe?man=netNglyc

Information


Unique identifier OMICS_02442
Name NetNGlyc
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Amino acid sequences.
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable

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. http://www.cbs.dtu.dk/cgi-bin/nph-runsafe?man=netNglyc

Publication for NetNGlyc

NetNGlyc citations

 (224)
library_books

Identification and characterization of the Fasciola hepatica sodium and chloride dependent taurine transporter

2018
PLoS Negl Trop Dis
PMCID: 5942844
PMID: 29702654
DOI: 10.1371/journal.pntd.0006428

[…] analysis was performed using MEGA 7 []. (neighbor-joining, 1000-replicate, bootstrap). The amino acid data were corrected for a gamma distribution (level set at 1.0) and with a Poisson correction.The NetNGlyc 1.0 Server (www.cbs.dtu.dk) was used to search for putative N-glycosylation sites in the final sequence of FhTauT []. We used the crystal structure of Hs SERT, derived from Coleman et al. (PD […]

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

[…] ignments and generate a sequence-similarity based phylogenetic 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(htt […]

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

[…] v. 4.1. The TargetP 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

Cloning and functional characterization of the DA2 receptor gene in Chinese mitten crab (Eriocheir sinensis)

2018
PLoS One
PMCID: 5858782
PMID: 29554147
DOI: 10.1371/journal.pone.0193999

[…] Protein phosphorylation sites were predicted using DISPHOS 1.3 (http://www.dabi.temple.edu/disphos/). N-glycosylation sites were predicted using the NetNGly 1.0 server (http://www.cbs.dtu.dk/services/NetNGlyc/). An amino acid multiple sequence alignment was performed with the ClustalX program, and phylogenetic tree was constructed using the neighbor-joining (NJ) method with1000 bootstraps in the M […]

library_books

Molecular characterization of US like and Asian non S INDEL strains of porcine epidemic diarrhea virus (PEDV) that circulated in Japan during 2013–2016 and PEDVs collected from recurrent outbreaks

2018
PMCID: 5852955
PMID: 29540176
DOI: 10.1186/s12917-018-1409-0

[…] created using the Kimura 2-parameter substitution method with a discrete gamma distribution (K2 + G). N-glycosylation sites were predicted using a service available on http://www.cbs.dtu.dk/services/NetNGlyc. Phosphorylation sites were predicted using the NetPhos 3.1 server (http://www.cbs.dtu.dk/services/NetPhos) and NetPhosBac 1.0 server (http://www.cbs.dtu.dk/services/NetPhosBac-1.0). Predicti […]

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

[…] the presence of glycosylphosphatidylinositol (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 ch […]

Citations

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NetNGlyc institution(s)
Center for Biological Sequence Analysis, Bio-Centrum Technical University of Denmark, Lyngby, Denmark
NetNGlyc funding source(s)
Supported by The Danish National Research Foundation.

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