Gene Designer

Gene Designer is a free bioinformatics software package.^[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.

Features

Gene Designer enables Molecular Biologists to capture the entire 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 for moving sequence elements within or between constructs (Patented feature)
• Search feature for Sequence motifs, Restriction sites and Open reading frames.
• Codon optimize for recombinant protein expression 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 for sequencing 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 their 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.

See also

• Bioinformatics
• Computational biology
• Gene synthesis
• Vector (molecular biology), Vector DNA, Cloning vector, Expression vector
• Restriction map
• Molecular cloning
• List of open source bioinformatics software

Educator and Student Use

This free software has been incorporated into Synthetic Biology, Systems Biology, Bioengineering and BioInformatics classroom and lab curricula. Students create and complete projects which capture the entire 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

References

1. ↑ 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. 
2. ↑ Villalobos, Alan; Welch, Mark; Minshull, Jeremy (2012). "Gene Synthesis". Methods in Molecular Biology 852. pp. 197–213. doi:10.1007/978-1-61779-564-0_15. ISBN 978-1-61779-563-3. PMID 22328435.  |chapter= ignored (help)
3. ↑ Welch, M; Villalobos, A; Gustafsson, C; Minshull, J (2011). "Designing genes for successful protein expression". Methods in enzymology 498: 43–66. doi:10.1016/B978-0-12-385120-8.00003-6. PMID 21601673. 

• US Patent 7,805,252. Systems and methods for designing and ordering polynucleotides. Gustafsson, Govindarajan, Ness, Villalobos and Minshull.

External links

Description of software

• Gene Designer homepage at DNA2.0

Tutorials

• 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

Other Software

• Geneious
• UGENE
• Vector NTI
• Clone manager
• MacVector