NetNGlyc protocols

View NetNGlyc computational protocol

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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


Add your version

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 in pipelines

 (4)
2017
PMCID: 5359912
PMID: 28320313
DOI: 10.1186/s12862-017-0910-6

[…] and phosphorylation) were predicted using online bioinformatic tools as described below and by comparison to the squid and bovine rhodopsins []. putative n-glycosylation sites were identified using netnglyc 1.0 (http://www.cbs.dtu.dk/services/netcglyc/) and palmitoylation sites were predicted with css-palm 3.0 (http://csspalm.biocuckoo.org/). putative phosphorylation sites were identified […]

2017
PMCID: 5623054
PMID: 29018364
DOI: 10.3389/fphys.2017.00744

[…] fly splice site prediction tool (http://www.fruitfly.org/seq_tools/splice.html). the intracellular and n-glycosylation sites were predicted using neyglyc 1.0 server (http://www.cbs.dtu.dk/services/netnglyc/) and the intracellular phosphorylation sites were predicted using netphos 3.1 server (http://www.cbs.dtu.dk/services/netphos/). palmitoylation of cysteine residues were predicted […]

2015
PMCID: 4770211
PMID: 26590257
DOI: 10.1093/nar/gkv1135

[…] of s. cereviseae, a. thaliana, o. saitva subsp. japonica, c. elegans, d. melanogaster, d. rerio, g. gallus and h. sapiens. ptms were predicted with freely available web tools netphos 2.0 (), netnglyc 1.0 (), pmes () and pail () with default parameters. a stretch of 30 residues in mediator complex subunits was considered as ptm hotspot if the fraction of predicted ptm sites […]

2014
PMCID: 4066178
PMID: 24584662
DOI: 10.1007/s11033-014-3298-z

[…] motifs are also present in the two sequences. the netphos 2.0 tool [] identified 20 putative phosphorylation sites in f1 and 28 in f2. on the basis of the consensus sequences asn-xaa-ser/thr, the netnglyc 1.0 prediction tool revealed four and three potential n-glycosylated sites in f1 and f2, respectively (fig. s1)., a search of the uniprotkb/swiss-prot database revealed that the both two new […]


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NetNGlyc in publications

 (639)
PMCID: 5954268
PMID: 29764421
DOI: 10.1186/s12864-018-4461-z

[…] site with pattern ngtr at sites 136–139 was introduced by the mutations s136n and i138t, and the potential of nnty at site 493 to be n-glycosylated is also likely to increase as predicted by netnglyc []. it has been reported that glycosylation of ha and na is associated with host specificity, virulence and human immune response. thus, glycosylation has been taken as an important way […]

PMCID: 5942844
PMID: 29702654
DOI: 10.1371/journal.pntd.0006428

[…] 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. […]

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

[…] that was reported from argentina [] (accession number: ay333364)., n-linked 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 […]

PMCID: 5932398
PMID: 29755357
DOI: 10.3389/fphar.2018.00426

[…] with the signalp 4.1 algorithm (petersen et al., ) via a web resource., the primary sequences of human, mouse, and cheetah lcn2 proteins were analyzed for potential n-glycosylation site using the netnglyc n-glycosylation site predictor with the default parameter settings., the hydrophobic cluster analysis of the lcn2 protein from different species was done with a web resource for structural […]

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

[…] 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 […]


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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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