cNLS Mapper protocols

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cNLS Mapper specifications

Information


Unique identifier OMICS_13510
Name cNLS Mapper
Interface Web user interface
Restrictions to use None
Input data A single amino acid sequence
Input format FASTA
Output data A result page including the input sequence with highlighted predicted NLS(s), list of monopartite and bipartite NLSs, their sequence, positions in the protein, and calculated scores
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Shunichi Kosugi <>

Publications for cNLS Mapper

cNLS Mapper in pipelines

 (9)
2018
PMCID: 5861215
PMID: 29593700
DOI: 10.3389/fmicb.2018.00468

[…] and 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 […]

2017
PMCID: 5210121
PMID: 28101087
DOI: 10.3389/fmicb.2016.02140

[…] the ncbi blastp program, and potential phosphorylation and glycosylation sites were determined with netphos 2.0 () and netnglyc1.0, respectively. the nuclear localization signals was predicted by cnls mapper (). sequence alignments of the nucleotide and predicted amino acids of the novel and other plant rhabdoviruses were carried out in clustal w. phylogenetic trees were generated […]

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

[…] dbd domain and (hr-a/b) domain in the putative peanut hsfs. candidate proteins without integrated dbd domain 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 […]

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

[…] page ruler protein 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 secondary structure prediction and alignment of cacv (km589494), tswv nsm (qld-1255, unpublished), tmv p30 (nc_001367.1), and tvcv p30 (u03387) were carried […]

2016
PMCID: 5019492
PMID: 27618178
DOI: 10.1371/journal.pone.0162708

[…] online prediction tool (http://www.med.muni.cz/9aatad/index.php) [,]. we selected the “most stringent pattern” option to identify 9aatad motifs in nhr-49 isoform c. nls prediction was performed with cnls mapper (http://nls-mapper.iab.keio.ac.jp/cgi-bin/nls_mapper_form.cgi) []., all in silico analysis was performed using accelrys discoverystudio v4.1 (biovia). the protein sequences for the five […]


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cNLS Mapper in publications

 (123)
PMCID: 5942036
PMID: 29770142
DOI: 10.3389/fpls.2018.00562

[…] computational algorithms to search for the presence of putative nuclear localization signals (nls) within the predicted sequences (minus signal peptide) of these proteins, namely nlspredict (), cnls mapper (), nlstradamus (), and wolf psort (). all nine of the nuclear-targeted checs possessed an nls that was predicted by two or more different algorithms (supplementary table ). in contrast, […]

PMCID: 5882135
PMID: 29614079
DOI: 10.1371/journal.pgen.1007287

[…] central nucleotide-binding (nb) site, and a leucine-rich repeat (lrr) region, typical of many nlr proteins. a nuclear localization signal (nls) was predicted in sr21 between amino acids 141 and 152 (cnls mapper http://nls-mapper.iab.keio.ac.jp/cgi-bin/nls_mapper_form.cgi)., comparing different transcripts and genomic sequences, we identified a 210-bp 5’ untranslated region (utr) and a 2,159-bp […]

PMCID: 5940170
PMID: 29593073
DOI: 10.1534/g3.118.200172

[…] that vps74 plays a more direct role in the nucleus, since vps74-gfp localizes to the nucleus, as well as the cytoplasm (figure s5) (). indeed, using two nuclear localization prediction programs (cnls mapper and nucpred), vps74 is predicted to have a weak nuclear localization signal in its n-terminus (; ; ). we conclude that vps74 regulates the fitness of yku70δ cells independently of sac1. […]

PMCID: 5874906
PMID: 29559568
DOI: 10.1128/mBio.00301-18

[…] domains, tgtkl protein sequences were searched against the pfam database (v. 31.0; http://pfam.xfam.org/) with an e value cutoff of 1 × 10−5 (, ). putative nls sequences were identified using the cnls mapper tool () and were considered to represent high confidence when the score was ≥10 ()., tgtkl1 to tgtkl6 were endogenously tagged at their c terminus using the methods described in reference […]

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

[…] and 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 […]


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cNLS Mapper institution(s)
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan; Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan; Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama, Ikoma, Nara, Japan
cNLS Mapper funding source(s)
This work was supported by grants from Yamagata Prefectural Government and Tsuruoka City and from the Ministry of Agriculture, Forestry, and Fisheries of Japan (Rice Genome Project SY-1114).

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