NetPlantGene statistics

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Citations per year

Number of citations per year for the bioinformatics software tool NetPlantGene
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Tool usage distribution map

This map represents all the scientific publications referring to NetPlantGene per scientific context
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Associated diseases

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Popular tool citations

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Protocols

NetPlantGene specifications

Information


Unique identifier OMICS_09617
Name NetPlantGene
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana

Maintainer


  • person_outline Soren Bruk

Publication for NetPlantGene

NetPlantGene citations

 (7)
library_books

CLE peptide encoding gene families in Medicago truncatula and Lotus japonicus, compared with those of soybean, common bean and Arabidopsis

2017
Sci Rep
PMCID: 5570945
PMID: 28839170
DOI: 10.1038/s41598-017-09296-w

[…] which could be the likely start codon. The modified sequence was re-entered into SignalP and a signal peptide was detected in most instances. Possible intron boundary sites were identified using the NetPlantGene Server (http://www.cbs.dtu.dk/services/NetPGene/), and the nucleotide splice sites and resulting prepropeptides were compared with orthologous sequences. Sequence logo graphs of the CLE d […]

library_books

Targeting a heterologous protein to multiple plant organelles via rationally designed 5′ mRNA tags

2013
J Biol Eng
PMCID: 3847293
PMID: 24011257
DOI: 10.1186/1754-1611-7-20

[…] P (smGFP) using Gibson assembly []. This modified GFP contains three site-directed mutations that increase the protein’s solubility and fluorescence intensity []. Based on splice site prediction with NetPlantGene [], we predicted that the processed spliceforms of TriTag-1 and TriTag 2 encodes for GFP variants containing regions for chloroplast targeting, peroxisomal targeting or neither. Splicefor […]

library_books

The Arabidopsis thaliana MHX gene includes an intronic element that boosts translation when localized in a 5′ UTR intron

2013
J Exp Bot
PMCID: 3808313
PMID: 24006416
DOI: 10.1093/jxb/ert235

[…] wn later on that elimination of this potential cryptic splice site resulted in full and accurate splicing of the CAT1 intron (). Prediction of potential cryptic splice sites was carried out using the NetPlantGene Server (http://www.cbs.dtu.dk/services/NetPGene/). The synthesized DNA fragment was used to replace the 5′ UTR and LI between the BglII site of the promoter and the Mva1269I site of GUS. […]

library_books

The Role of Canonical and Noncanonical Pre mRNA Splicing in Plant Stress Responses

2012
Biomed Res Int
PMCID: 3591102
PMID: 23509698
DOI: 10.1155/2013/264314

[…] ng-specific signs. Splice sites in the Arabidopsis DNA and DNA of other eukaryotes can be detected using the GeneSplicer Web Interface [] found at http://www.cbcb.umd.edu/software/GeneSplicer/ or the NetPlantGene Server [] found at http://www.cbs.dtu.dk/services/NetPGene/. To compile and visualize the evidence for alternative splicing in plants, a comprehensive web-interfaced database ASIP [] foun […]

call_split

Diversification, Biogeographic Pattern, and Demographic History of Taiwanese Scutellaria Species Inferred from Nuclear and Chloroplast DNA

2012
PLoS One
PMCID: 3511331
PMID: 23226402
DOI: 10.1371/journal.pone.0050844
call_split See protocol

[…] ons of each sequence were queried in the Nucleotide collection database at the National Center for Biotechnology Information website using the Nucleotide Basic Local Alignment Search Tool program and NetPlantGene server at the Center for Biological Sequence Analysis website (www.cbs.dtu.dk/services/NetPGene/). All sequences were deposited in the NCBI nucleotide sequence database under the followin […]

library_books

Fast splice site detection using information content and feature reduction

2008
BMC Bioinformatics
PMCID: 2638148
PMID: 19091031
DOI: 10.1186/1471-2105-9-S12-S8

[…] identify true splice sites among numerous false ones. Weight matrix methods (WMM) and methods based on Markov models are popular methods of this category. WMM was successfully adopted in methods like NetPlantGene [] and NNSplice []. Salzberg et al. and Zhang et al. [,], used a linear first order Markov model (MM1) also known as the weight array method (WAM) and they have achieved a good splice sit […]


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NetPlantGene institution(s)
Center for Biological Sequence Analysis, The Technical University of Denmark, DK, Lyngby, Denmark; Laboratoire Associé de l'INRA, VIB, University of Gent, Gent, Belgium

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