NLStradamus statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool NLStradamus
info

Tool usage distribution map

This map represents all the scientific publications referring to NLStradamus per scientific context
info info

Associated diseases

This word cloud represents NLStradamus usage per disease context
info

Popular tool citations

chevron_left Subcellular localization prediction chevron_right
Want to access the full stats & trends on this tool?

Protocols

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

Download


download.png
galaxy.png
conda.png

Versioning


No version available

Maintainer


  • person_outline Alan M. Moses

Publication for NLStradamus

NLStradamus citations

 (61)
library_books

Subcellular Localization Screening of Colletotrichum higginsianum Effector Candidates Identifies Fungal Proteins Targeted to Plant Peroxisomes, Golgi Bodies, and Microtubules

2018
Front Plant Sci
PMCID: 5942036
PMID: 29770142
DOI: 10.3389/fpls.2018.00562

[…] nal 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 the remaini […]

library_books

Cryptochrome Regulates Circadian Locomotor Rhythms in the Small Brown Planthopper Laodelphax striatellus (Fallén)

2018
Front Physiol
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 Ill […]

library_books

Divergent bornaviruses from Australian carpet pythons with neurological disease date the origin of extant Bornaviridae prior to the end Cretaceous extinction

2018
PLoS Pathog
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 sig […]

library_books

Kinesin 1 regulates cilia length through an interaction with the Bardet Biedl syndrome related protein CCDC28B

2018
Sci Rep
PMCID: 5813027
PMID: 29445114
DOI: 10.1038/s41598-018-21329-6

[…] 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. We […]

library_books

Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines

2018
Sci Rep
PMCID: 5802810
PMID: 29410430
DOI: 10.1038/s41598-018-20536-5

[…] n 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 sequences […]

library_books

Secretome Characterization and Correlation Analysis Reveal Putative Pathogenicity Mechanisms and Identify Candidate Avirulence Genes in the Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici

2017
Front Microbiol
PMCID: 5732408
PMID: 29312156
DOI: 10.3389/fmicb.2017.02394

[…] l., ).The PST-78 predicted secretome was annotated using Blast2GO v3.3 (Conesa et al., ). LocTree3 (Goldberg et al., ), and NucPred (Brameier et al., ) were used to predict subcellular localizations. NLStradamus (Nguyen et al., ) was used to predict Nuclear Localization Signals. PFAM domains were annotated using HMMSCAN searches against the PFAM database in HmmerWeb v2.3.3 (Finn et al., ). To dete […]


Want to access the full list of citations?
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.

NLStradamus reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review NLStradamus