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Gene Designer specifications

Information


Unique identifier OMICS_10859
Name Gene Designer
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Publication for Gene Designer

Gene Designer citations

 (12)
library_books

One pot synthesis of GDP‐mannose by a multi‐enzyme cascade for enzymatic assembly of lipid‐linked oligosaccharides

2017
Biotechnol Bioeng
PMCID: 5765510
PMID: 28922469
DOI: 10.1002/bit.26454

[…] ALG1 (Δ4‐105) the bases 4–105, coding for the transmembrane domain, were deleted according to Revers, Wilson, Webberley, and Flitsch (). All nucleotide sequences were codon usage optimized (Software: Gene Designer, DNA 2.0, Menlo Park, CA) for expression in E. coli. Restriction sites for subcloning into pET‐28a (+) were added to the sequences as follows: ppa (NcoI, XhoI), ppk2 (NdeI, SacI), and AL […]

library_books

Predicting synonymous codon usage and optimizing the heterologous gene for expression in E. coli

2017
Sci Rep
PMCID: 5577221
PMID: 28855614
DOI: 10.1038/s41598-017-10546-0

[…] system, the gene should be designed based on the codon usage pattern of the host strain of the expression system and the codon selection constraints of the target gene–.Many methods, including COOL, Gene Designer, Gene composer, JCat, COStar and OPTIMIZER, have been proposed to design heterologous genes which are expected to be efficiently expressed in the host organism. Based on our knowledge, t […]

call_split

Heterologous expression of Aspergillus aculeatus endo polygalacturonase in Pichia pastoris by high cell density fermentation and its application in textile scouring

2017
BMC Biotechnol
PMCID: 5314705
PMID: 28209146
DOI: 10.1186/s12896-017-0334-9
call_split See protocol

[…] hout a signal peptide was synthesized based on the coding sequence of A. aculeatus ATCC16872. The codon usage was analyzed by Codon Usage Analyzer [] and optimized for expression in P. pastoris using Gene Designer Software []. The optimized gene was synthesized by Genescript (Piscataway, NJ, USA). Escherichia coli DH5α was used as a host for plasmid propagation. E. coli was propagated in low salt […]

library_books

Molecular Cloning Designer Simulator (MCDS): All in one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects

2016
Metab Eng Com
PMCID: 5779711
PMID: 29468123
DOI: 10.1016/j.meteno.2016.05.003

[…] Clone Manager (Software), which could be used for importing sequences and checking DNA maps; NEBcutter () for analyzing restriction sites; Primer Premier () for designing primers; GeneDesign 3.0 (), Gene Designer (), OPTIMIZER (), DNAWorks () or Gene2Oligo () for optimizing gene codons for synthesis; and BioEdit ( ) for viewing and confirming sequencing data. Cloning design required use of two or […]

library_books

Computational Tools and Algorithms for Designing Customized Synthetic Genes

2014
Front Bioeng Biotechnol
PMCID: 4186344
PMID: 25340050
DOI: 10.3389/fbioe.2014.00041

[…] Gene Designer (Villalobos et al., ) is a stand-alone software that facilitates the construction of novel genetic material through an intuitive drag-and-drop approach to add and remove genetic elements […]

library_books

In Situ Overlap and Sequence Synthesis During DNA Assembly

2013
ACS Synth Biol
PMCID: 3874219
PMID: 24161008
DOI: 10.1021/sb400067v

[…] The constructs were designed using the Gene Designer software and the CLC Main workbench. […]

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Gene Designer institution(s)
DNA 20, Inc, Menlo Park, CA, USA

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