title: R2oDNA designer: computational design of biologically neutral synthetic DNA sequences.
abstract: R2oDNA Designer is a web application that stochastically generates orthogonal sets of synthetic DNA sequences designed to be biologically neutral. Biologically neutral sequences may be used for directing efficient DNA assembly by overlap-directed methods, as a negative control for functional DNA, as barcodes, or potentially as spacer regions to insulate biological parts from local context. The software creates optimized sequences using a Monte Carlo simulated annealing approach followed by the elimination of sequences homologous to host genomes and commonly used biological parts. An orthogonal set is finally determined by using a network elimination algorithm. Design constraints can be defined using either a web-based graphical user interface (GUI) or uploading a file containing a set of text commands.
authors.affiliation: Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, United Kingdom.
authors.forename: Arturo
authors.initials: A
authors.lastname: Casini
authors.forename: Georgia
authors.initials: G
authors.lastname: Christodoulou
authors.forename: Paul S
authors.initials: PS
authors.lastname: Freemont
authors.forename: Geoff S
authors.initials: GS
authors.lastname: Baldwin
authors.forename: Tom
authors.initials: T
authors.lastname: Ellis
authors.forename: James T
authors.initials: JT
authors.lastname: MacDonald
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D016678:Genome; D009010:Monte Carlo Method; D012984:Software; D013269:Stochastic Processes; D014584:User-Computer Interface
chemical_list: D004247:DNA