Gene Designer

Gene Designer
Gene Designer
	Gene Designer Sequence View enables manipulation of sequence elements, codon choices, and oligonucleotide positions. Rapidly search for sequence motifs, restriction sites, and open reading frames.
Developer(s)	ATUM
Initial release	2006; 19 years ago
Stable release	2.01.191 / October 9, 2015; 9 years ago
Operating system	Windows, macOS, Linux
Platform	x86, x86-64
Available in	English
Type	Molecular biology toolkit
License	Freeware, registration required
Website	www.atum.bio/resources/tools/gene-designer

Gene Designer is a computer software package for bioinformatics.^[1]^[2] It is used by molecular biologists from academia, government, and the pharmaceutical, chemical, agricultural, and biotechnology industries to design,^[3] clone, and validate genetic sequences. It is proprietary software, released as freeware needing registration.

Features

Gene Designer enables molecular biologists to manage the full gene design process in one application, using a range of design tools.

Algorithms for in silico cloning, codon optimization, back translation, and primer design
Graphic molecular View to display, annotate, and edit constructs
Customizable database to store, manage, and track genetic elements, genes, and constructs
Drag and drop interface to move sequence elements within or between constructs (patented feature)
Search feature for sequence motifs, restriction sites, and open reading frames
Codon optimize for recombinant protein production in any organism using multiple algorithms
Remove or add restriction sites or other sequence motifs
Recode open reading frames
Check translation frames and fusion junctions
Design oligonucleotides to sequence primers, includes a real time melting point calculator
Cloning tool with drag and drop ability to cut, combine, and clone insert and vector

Gene Designer clones with a drag and drop feature. Users can drag a vector and insert into the Cloning Tool; cut, combine and clone. Gene Designer assembles a clone that can then be dropped directly into a project.

Educator and student use

This free software has been incorporated into classroom and lab curricula for synthetic biology, systems biology, bioengineering, and bioinformatics. Students create and complete projects which manage the full gene design process in one application, using a range of design tools.

Examples of use in curricula:

Synthetic Photonics Course; Utah State University, College of Engineering^[4]
Lab Project using Gene Designer 2.0^[5]
Systems Biology Lesson Overview^[6]
Synthetic Biology Lesson Overview^[7]
Student Projects^[8]

References

^ Villalobos, Alan; Ness, Jon E; Gustafsson, Claes; Minshull, Jeremy; Govindarajan, Sridhar (2006). "Gene Designer: A synthetic biology tool for constructing artificial DNA segments". BMC Bioinformatics. 7: 285. doi:10.1186/1471-2105-7-285. PMC 1523223. PMID 16756672.
^ Villalobos, Alan; Welch, Mark; Minshull, Jeremy (2012). "In Silico Design of Functional DNA Constructs". In Peccoud, Jean (ed.). Gene Synthesis: Methods and Protocols. Methods in Molecular Biology. Vol. 852. pp. 197–213. doi:10.1007/978-1-61779-564-0_15. ISBN 978-1-61779-563-3. PMID 22328435.
^ Welch, M; Villalobos, A; Gustafsson, C; Minshull, J (2011). "Designing genes for successful protein expression". In Voigt, Christopher (ed.). Synthetic Biology, Part B: Computer Aided Design and DNA Assembly. Methods in Enzymology. Vol. 498. pp. 43–66. doi:10.1016/B978-0-12-385120-8.00003-6. ISBN 9780123851208. PMID 21601673.
^ [1]
^ [2]
^ [3]
^ [4]
^ [5]