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NLStradamus specifications

Information


Unique identifier OMICS_13513
Name NLStradamus
Interface Web user interface
Restrictions to use None
Input data A protein sequence or multiple sequences, HMM state emission and transition frequencies, prediction type
Input format FASTA, TXT
Output data Predicted sequences, a table that you can export with the start and stop positions of predicted NLS, an image with the NLS boxed over a line representing the protein sequence, a graphical representation of its distribution (only applicable to posterior probability).
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Alan M. Moses <>

Information


Unique identifier OMICS_13513
Name NLStradamus
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Protein sequence
Input format FASTA
Output data The gene ID followed by the predicted sequences.
Operating system Unix/Linux
Programming languages C++, Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.8
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Alan M. Moses <>

Publication for NLStradamus

NLStradamus in pipelines

 (4)
2017
PMCID: 5343943
PMID: 28216607
DOI: 10.3390/ijms18020409

[…] services/signalp/) was used for discriminating signal peptides. sequence translation was done at http://web.expasy.org/translate/. nls sequence domain of pitg_22798 was predicted by nlstradamus with a prediction cutoff value of 0.6. nlstradamus uses hidden markov models (hmms) (http://www.moseslab.csb.utoronto.ca/nlstradamus/) to predict novel nlss in proteins []., […]

2017
PMCID: 5573122
PMID: 28846714
DOI: 10.1371/journal.pone.0183567

[…] to exclude sequences with transmembrane domains, er-retention signal and gpi anchors, respectively. the secretory proteins with nuclear localization signal were identified using nlstradamus (v1.8) [], while putative effector proteins were predicted through effectorp (v1.0) []. carbohydrate active enzymes (cazymes) were identified by hmmer (v3.1b1, http://hmmer.janelia.org/) […]

2016
PMCID: 5062187
PMID: 27790231
DOI: 10.3389/fpls.2016.01516

[…] web portal (goujon et al., ). alignments are displayed using the “rtf new” output of boxshade (http://www.ch.embnet.org/software/box_form.html). the candidate trunctale nls was identified using nlstradamus (nguyen ba et al., )., expression constructs were transformed into e. coli rosetta plyss (de3) cells (emd millipore, billerica, ma). single colonies were grown overnight in 5 ml of lb […]

2013
PMCID: 3792188
PMID: 24109552
DOI: 10.7717/peerj.167

[…] output (; ), and signalp v3.0, which produces space separated output (), required minor conversion to tab-separated output. other tools, such as the nuclear localisation signal prediction tools nlstradamus () and nod (; ), produced no suitable output. in these cases, a tabular output option was added to each tool, following discussion with the authors. some tools, such as ncbi blast+, […]


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NLStradamus in publications

 (58)
PMCID: 5942036
PMID: 29770142
DOI: 10.3389/fpls.2018.00562

[…] 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, among […]

PMCID: 5835671
PMID: 29541034
DOI: 10.3389/fphys.2018.00149

[…] accession numbers of genes used are listed in table . smart (letunic et al., ) and cdd (marchler-bauer et al., ) were used for motif prediction. nuclear localization signals (nlss) were predicted by nlstradamus based on an analysis of the residues frequencies of known nlss using hidden markov models (hmms) (nguyen ba et al., ). schematic representation of cryptochrome proteins was drawn using […]

PMCID: 5834213
PMID: 29462190
DOI: 10.1371/journal.ppat.1006881

[…] identified in the bodv-1 n, p, and x proteins [–]. none of these nls are obviously conserved in the corresponding jcpv and swcpv proteins (except for x, see below, and – figs), nor did nlsmapper or nlstradamus predict nls in these regions. however, these tools both predicted a nls at another position in jcpv and swcpv p (58-kkikrkrett in jcpv p, and 59-kkakrkreiv in swcpv p; )., nuclear export […]

PMCID: 5813027
PMID: 29445114
DOI: 10.1038/s41598-018-21329-6

[…] 5, to follow up on the previous finding we decided to evaluate whether a predicted nuclear localization signal (nls), encompassing residues 4 to 10 in ccdc28b (http://www.moseslab.csb.utoronto.ca/nlstradamus/http://elm.eu.org; fig. ,,, is functional. this nls is conserved between human and zebrafish and therefore we deleted residues 4 to 10 (δ4–10) in both orthologs to generate nls mutants. […]

PMCID: 5802810
PMID: 29410430
DOI: 10.1038/s41598-018-20536-5

[…] the ppj2 and pj2 life stages of the nematode, with those peptides showing a minimum 4-fold up-regulation into the pj2 life stage retained. finally, nuclear localization signals were predicted using nlstradamus. for n-preffector based prediction, predicted peptides were run through a machine-learning algorithm trained on 72 known h. glycines effector sequences and 150 known non-effector […]


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NLStradamus institution(s)
Department of Cell & Systems Biology, University of Toronto, Toronto, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
NLStradamus funding source(s)
This work was supported by a research award from the Center for the Analysis of Genome Evolution and Function (CAGEF) and by a Canadian Foundation for Innovation infrastructure grant.

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