title: Gene Designer: a synthetic biology tool for constructing artificial DNA segments.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  Gene Designer is an expandable Synthetic Biology workbench suitable for molecular biologists interested in the de novo creation of genetic constructs.
authors.affiliation: DNA 2.0, Inc., 1430 O'Brien Drive Suite E, Menlo Park, CA 94025, USA. avillalobos@dna20.com
authors.forename: Alan
authors.initials: A
authors.lastname: Villalobos
authors.forename: Jon E
authors.initials: JE
authors.lastname: Ness
authors.forename: Claes
authors.initials: C
authors.lastname: Gustafsson
authors.forename: Jeremy
authors.initials: J
authors.lastname: Minshull
authors.forename: Sridhar
authors.initials: S
authors.lastname: Govindarajan
mesh_terms: D001483:Base Sequence; D017076:Computer-Aided Design; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D015195:Drug Design; D005813:Genes, Synthetic / Q000235:genetics*; D005818:Genetic Engineering / Q000379:methods*; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D049490:Systems Biology / Q000379:methods*; D014584:User-Computer Interface
chemical_list: D004247:DNA