NetPlantGene protocols

View NetPlantGene computational protocol

NetPlantGene statistics

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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 in pipeline

2010
PMCID: 3036070
PMID: 21637618
DOI: 10.1590/S1415-47572010000100024

[…] aligned at the amino acid level and subsequently, the nucleic acid sequences were aligned according to the amino acid sequences. intron prediction was done by using the intron prediction program at netplantgene server., phylogenetic analysis was carried out using the neighbour joining (nj) and maximum parsimony (mp) methods implemented in mega3 (). the intron sequence of acpks was removed […]


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NetPlantGene in publications

 (7)
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 […]

PMCID: 3847293
PMID: 24011257
DOI: 10.1186/1754-1611-7-20

[…] (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. […]

PMCID: 3808313
PMID: 24006416
DOI: 10.1093/jxb/ert235

[…] 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. […]

PMCID: 3591102
PMID: 23509698
DOI: 10.1155/2013/264314

[…] 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 [] […]

PMCID: 3511331
PMID: 23226402
DOI: 10.1371/journal.pone.0050844

[…] 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 […]


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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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