2.01.191 / October 9, 2015
|Operating system||Windows, macOS, Linux|
|Type||Molecular biology toolkit|
|License||Freeware, registration required|
Gene Designer is a computer software package for bioinformatics. It is used by molecular biologists from academia, government, and the pharmaceutical, chemical, agricultural, and biotechnology industries to design, clone, and validate genetic sequences. It is proprietary software, released as freeware needing registration.
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
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 Biophotonics Course; Utah State University, College of Engineering
- Lab Project using Gene Designer 2.0
- Systems Biology Lesson Overview
- Synthetic Biology Lesson Overview
- Student Projects
- Computational biology
- Gene synthesis
- Vector (molecular biology), Vector DNA, Cloning vector, Expression vector
- Restriction map
- Molecular cloning
- List of open source bioinformatics software
- 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. PMC . PMID 16756672. doi:10.1186/1471-2105-7-285.
- Villalobos, Alan; Welch, Mark; Minshull, Jeremy (2012). "Gene Synthesis". Methods in molecular biology (Clifton, N.J.). Methods in Molecular Biology. 852: 197–213. ISBN 978-1-61779-563-3. PMID 22328435. doi:10.1007/978-1-61779-564-0_15.
- Welch, M; Villalobos, A; Gustafsson, C; Minshull, J (2011). "Designing genes for successful protein expression". Methods in enzymology. Methods in Enzymology. 498: 43–66. ISBN 9780123851208. PMID 21601673. doi:10.1016/B978-0-12-385120-8.00003-6.
- US Patent 7,805,252. Systems and methods for designing and ordering polynucleotides. Gustafsson, Govindarajan, Ness, Villalobos and Minshull.
- Gene Designer Webinar: demonstrates how to design gene sequences, how to remove or add restriction sites or other motifs, primer design, cloning scheme, and other features.
- BioBrick Video Tutorial using Gene Designer 2.0 from Utah State University
- Gene Designer User Video
- Cloning Tool User Video
- Gene Designer Help
- Gene Designer Tutorial from Utah State University