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GenDecoder specifications

Information


Unique identifier OMICS_19575
Name GenDecoder
Interface Web user interface
Restrictions to use None
Input data An animal mitochondrial genome.
Computer skills Basic
Version 1.6
Stability Stable
Maintained No

Maintainer


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Publications for GenDecoder

GenDecoder citations

 (18)
library_books

Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida

2018
BMC Evol Biol
PMCID: 5924465
PMID: 29703131
DOI: 10.1186/s12862-018-1186-1

[…] MITOS (which implements MITFI) [].Base compositions were computed with Geneious (version R6.1). Potential modifications of the mold genetic code were investigated both manually and with the webserver GenDecoder v.1.6 [] using default parameters.Perfect repeats having a repeat unit longer than 20 bp were searched with the REPFIND webserver (http://zlab.bu.edu/repfind/form.html) [] under default set […]

library_books

Naturally acquired antibody responses to more than 300 Plasmodium vivax proteins in three geographic regions

2017
PLoS Negl Trop Dis
PMCID: 5614652
PMID: 28892517
DOI: 10.1371/journal.pntd.0005888

[…] bstrate layers. Crude WGCF expressed BirA (1 μl) was added to the translation layer. In vitro transcription and cell-free protein synthesis for the P. vivax protein library were carried out using the GenDecoder 1000 robotic synthesizer (CellFree Sciences) [, ]. Based on previous studies, the WGCF system can synthesize biotinylated plasmodial protein ranging from 0.3 μg/mL to 26.5 μg/mL [,]. Expres […]

library_books

Immunoscreening of Plasmodium falciparum proteins expressed in a wheat germ cell free system reveals a novel malaria vaccine candidate

2017
Sci Rep
PMCID: 5380959
PMID: 28378857
DOI: 10.1038/srep46086

[…] wheat germ cell-free expressed BirA (1 μl) was added to the translation layer. In vitro transcription and cell-free protein synthesis for the P. falciparum protein library were carried out using the GenDecoder 1000 robotic synthesizer (CellFree Sciences) as previously described. Expression of the proteins was confirmed by western blotting using FITC- or HRP-conjugated streptavidin (ThermoFisher S […]

library_books

Mitochondrial Genomes of Kinorhyncha: trnM Duplication and New Gene Orders within Animals

2016
PLoS One
PMCID: 5068742
PMID: 27755612
DOI: 10.1371/journal.pone.0165072

[…] (A − T) / (A + T) and GC-skew = (G − C) / (G + C) [], where the letters stand for the absolute number of the corresponding nucleotides in the sequences. Genetic code and codon usage were analyzed by GenDecoder v1.6 [] and FACIL [] web tools. Characterization of codon usage bias was calculated with the BioEdit program []. […]

library_books

H11/HSPB8 Restricts HIV 2 Vpx to Restore the Anti Viral Activity of SAMHD1

2016
Front Microbiol
PMCID: 4904303
PMID: 27379031
DOI: 10.3389/fmicb.2016.00883

[…] n method was also described previously (, ; ). Briefly, DNA templates containing a biotin-ligating sequence (bls) were amplified by split-PCR using cDNAs and corresponding primers, and then used in a GenDecoder protein production system (Cell Free Science, Ehime, Japan). For synthesis of HIV-2 Vpx protein, Vpx genes derived from the pGL-AN proviral plasmid were generated by split-PCR and used as t […]

library_books

Establishment of a Wheat Cell Free Synthesized Protein Array Containing 250 Human and Mouse E3 Ubiquitin Ligases to Identify Novel Interaction between E3 Ligases and Substrate Proteins

2016
PLoS One
PMCID: 4889105
PMID: 27249653
DOI: 10.1371/journal.pone.0156718

[…] The protein array containing the 258 E3s was produced by using the robotic synthesizer GenDecoder 1000 (CellFree Sciences, Yokohama, Japan) as described previously []. The biotinylated proteins were synthesized with a bilayer method that used 1 μL crude biotin ligase (BirA) produced by […]

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GenDecoder institution(s)
Departamento de Genética, Bioquímica e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain

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