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Visual gene developer specifications

Information


Unique identifier OMICS_08711
Name Visual gene developer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Computer skills Medium
Version 1.7
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Sang-Kyu Jung

Publication for Visual gene developer

Visual gene developer citations

 (7)
library_books

A novel B and helper T cell epitopes based prophylactic vaccine against Echinococcus granulosus

2017
PMCID: 5915707
PMID: 29713601
DOI: 10.15171/bi.2018.06

[…] nslation initiation and elongation steps. Thus, the Codon Adaptation Index (CAI), G/C content, mRNA secondary structure and Gibbs free energy (∆G) of the optimized mRNA structure were performed using Visual Gene Developer v1.7 program. The codon frequency table of E. coli K12, which is postulated for codon and mRNA analysis, was directly imported from CUTG (Codon Usage Tabulated from GenBank) webs […]

call_split

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

2016
PLoS One
PMCID: 5125587
PMID: 27893824
DOI: 10.1371/journal.pone.0166260
call_split See protocol

[…] ol and has greater correlations with protein abundance compared with other indicators []. The tAI value of ZIKV polyprotein-coding region based on the tRNA copy number of H. sapiens was calculated by Visual Gene Developer []. […]

library_books

Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha

2016
Bioinform Biol Insights
PMCID: 5034883
PMID: 27688709
DOI: 10.4137/BBI.S38192

[…] codon usage was not considered to be conserved among these species. Putative optimal codons are of paramount significance in enhancing heterologous gene expression and, moreover, the a software named Visual Gene Developer improves the expression levels of a synthetic gene by adopting a codon optimization strategy., Hence, the identification of putative optimal codons in chaetognaths may help in st […]

library_books

Semicontinuous Bioreactor Production of Recombinant Butyrylcholinesterase in Transgenic Rice Cell Suspension Cultures

2016
Front Plant Sci
PMCID: 4814504
PMID: 27066048
DOI: 10.3389/fpls.2016.00412

[…] y3D promoter, signal peptide, and terminator sequences using GenScript (GenScript, Piscataway, NJ). The native human BChE coding sequence was codon optimized for expression in rice and analyzed using Visual Gene Developer (http://visualgenedeveloper.net). The sequence was modified without any changes in the amino acid sequence of the mature protein. The overall GC content of the DNA sequence was i […]

library_books

A Variant of GJD2, Encoding for Connexin 36, Alters the Function of Insulin Producing β Cells

2016
PLoS One
PMCID: 4784816
PMID: 26959991
DOI: 10.1371/journal.pone.0150880

[…] Jalview [] was used to generate the sequence alignment of WT Cx36 mRNA (681C) and of two allelic variants: variant 681C>T, previously known as 588C>T, and variant 462C>T, previously known as 369C>T. Visual Gene Developer 1.7 program [] was used to calculate the mRNA structure by employing the “mRNA structure (slow)” tool. […]

library_books

A new strategy to express the extracellular α amylase from Pyrococcus furiosus in Bacillus amyloliquefaciens

2016
Sci Rep
PMCID: 4768087
PMID: 26916714
DOI: 10.1038/srep22229

[…] the codon usage and mRNA structure of BAA. To mimic the codon usage of BAA, the rare codons were substituted according to the codon usage data of B. amyloliquefaciens DSM7. In this step, the Biosoft visual gene developer (VGD) was used to perform seven rounds of calculations. The calculations were performed 10 times in the first five rounds, 1000 times in the sixth round, and 2000 times in the se […]

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Visual gene developer institution(s)
Department of Chemical Engineering and Materials Science, University of California, Davis, Davis, CA, USA

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