NetNES protocols

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NetNES specifications

Information


Unique identifier OMICS_17911
Name NetNES
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Input format FASTA
Computer skills Basic
Version 1.1
Stability Stable
Maintained Yes

Maintainer


  • person_outline Soren Brunak <>

Publication for NetNES

NetNES in pipelines

 (18)
2018
PMCID: 5861215
PMID: 29593700
DOI: 10.3389/fmicb.2018.00468

[…] signalp were used to predict signal peptide cleavage sites (http://www.cbs.dtu.dk/services/signalp/). the nuclear localization and export signals were predicted by cnls mapper (kosugi et al., ) and netnes 1.1 (la cour et al., ), respectively. mapping of clean rna-seq reads from both wheat and leafhopper to the complete viral genome sequence as a reference was performed using the clc genomics […]

2017
PMCID: 5292572
PMID: 28220134
DOI: 10.3389/fpls.2017.00106

[…] and hr-a/b domain were removed. nls domains in peanut hsfs were predicted using cnls mapper software (http://nls-mapper.iab.keio.ac.jp/cgi-bin/nls_mapper_form.cgi). nes domains were predicted using netnes 1.1 server software (http://www.cbs.dtu.dk/services/netnes/). aha domains were predicted based on the conserved-type aha motif sequence fwxxf/l, f/i/l (kotak et al., ). protein isoelectric […]

2017
PMCID: 5322759
PMID: 28243526
DOI: 10.7717/peerj.2974

[…] was done using clustal omega (http://www.ebi.ac.uk/tools/msa/clustalo/) (; ) to show conservation of the domains in the selected organisms. the prediction of the nuclear export signal (nes) was by netnes (http://www.cbs.dtu.dk/services/netnes/) (). further analysis of protein sequences was performed with phyre2 (), a web portal for protein modelling, prediction, and analysis […]

2017
PMCID: 5387057
PMID: 28443083
DOI: 10.3389/fmicb.2017.00612

[…] ladder (thermo fisher scientific)., deduced amino acid sequences of cacv proteins were analyzed for potential nuclear localization (import) and nuclear export signals using cnls mapper () and netnes 1.1 server (). secondary structure prediction and alignment of cacv (km589494), tswv nsm (qld-1255, unpublished), tmv p30 (nc_001367.1), and tvcv p30 (u03387) were carried out using promals3d […]

2017
PMCID: 5469009
PMID: 28616073
DOI: 10.1186/s13068-017-0807-z

[…] signals (nls) in the amino acid sequences were determined using the nucpred (http://www.sbc.su.se/~maccallr/nucpred/) [] and predicted nuclear export signals (nes) were detected with the netnes 1.1 server (http://www.cbs.dtu.dk/services/netnes/) []., protein sequence identity of full-length pdr-1 (ncu09033) to rhar of a. niger (an13g00910) or a. nidulans (an5673), as well as trc1 […]


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NetNES in publications

 (121)
PMCID: 5936033
PMID: 29728113
DOI: 10.1186/s12917-018-1465-5

[…] nucleus during its early life cycle. in fact, we have not only predicted the presence of nuclear localization signals (nlss) with psort ii but also predicted nuclear exporting signals (ness) with netnes server (http://www.cbs.dtu.dk/services/netnes/). these putative nls motifs were within the amino acid sequence of vp1, which spanned from amino acid residues 3 to 19 (nls1) and 24 to 47 […]

PMCID: 5935713
PMID: 29728564
DOI: 10.1038/s41598-018-25007-5

[…] diffusion of tdp-43 out of the nucleus and thus may contribute to cytoplasmic mislocalization of tdp-43 in als and ftd patients., using bioinformatic nes prediction tools (nes finder 0.2 and netnes 1.1 server), we identified two putative crm1-dependent ness in each tdp-43 (at positions 222 and 239) and fus (at positions 289 and 301) (fig. ). nes-239 (iaqslcgedlii) in tdp-43 and nes-289 […]

PMCID: 5942036
PMID: 29770142
DOI: 10.3389/fpls.2018.00562

[…] or less than, the mean chec mw (11.45 kda, supplementary table ). in the case of chec30 and chec103, this localization was consistent with the detection of a putative nuclear export signal using the netnes prediction tool ()., the subcellular localizations determined experimentally by gfp-tagging the checs were compared with localizations predicted by the localizer tool () running in ‘effector […]

PMCID: 5861215
PMID: 29593700
DOI: 10.3389/fmicb.2018.00468

[…] signalp were used to predict signal peptide cleavage sites (http://www.cbs.dtu.dk/services/signalp/). the nuclear localization and export signals were predicted by cnls mapper (kosugi et al., ) and netnes 1.1 (la cour et al., ), respectively. mapping of clean rna-seq reads from both wheat and leafhopper to the complete viral genome sequence as a reference was performed using the clc genomics […]

PMCID: 5794737
PMID: 29391403
DOI: 10.1038/s41598-018-19766-4

[…] domains in ecbzip17 were observed using the simple modular architecture research tool (smart; http://smart.embl-heidelberg.de/). the leucine rich nuclear export signals (nes) were predicted by the netnes 1.1 server (http://www.cbs.dtu.dk/services/netnes/), whereas the nuclear localisation signal was predicted by the cnls mapper tool […]


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NetNES institution(s)
Center for Biological Sequence Analysis, Biocentrum-DTU, Technical University of Denmark, Lyngby; Department of Protein Chemistry, Institute of Molecular Biology, University of Copenhagen, Copenhagen, Denmark

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