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Gene Designer: a synthetic biology tool for constructing artificial DNA segments

Alan Villalobos, Jon E Ness, Claes Gustafsson*, Jeremy Minshull and Sridhar Govindarajan

Author Affiliations

DNA 2.0, Inc. 1430 O'Brien Drive Suite E, Menlo Park, CA 94025, USA

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BMC Bioinformatics 2006, 7:285  doi:10.1186/1471-2105-7-285

Published: 6 June 2006



Direct synthesis of genes is rapidly becoming the most efficient way to make functional genetic constructs and enables applications such as codon optimization, RNAi resistant genes and protein engineering. Here we introduce a software tool that drastically facilitates the design of synthetic genes.


Gene Designer is a stand-alone software for fast and easy design of synthetic DNA segments. Users can easily add, edit and combine genetic elements such as promoters, open reading frames and tags through an intuitive drag-and-drop graphic interface and a hierarchical DNA/Protein object map. Using advanced optimization algorithms, open reading frames within the DNA construct can readily be codon optimized for protein expression in any host organism. Gene Designer also includes features such as a real-time sliding calculator of oligonucleotide annealing temperatures, sequencing primer generator, tools for avoidance or inclusion of restriction sites, and options to maximize or minimize sequence identity to a reference.


Gene Designer is an expandable Synthetic Biology workbench suitable for molecular biologists interested in the de novo creation of genetic constructs.