Casini Arturo, Christodoulou Georgia, Freemont Paul S, Baldwin Geoff S, Ellis Tom, MacDonald James T
Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, United Kingdom.
ACS Synth Biol. 2014 Aug 15;3(8):525-8. doi: 10.1021/sb4001323. Epub 2014 Feb 11.
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.
R2oDNA Designer是一个网络应用程序，它能随机生成经设计具有生物中性的合成DNA序列正交集。生物中性序列可用于通过重叠定向方法指导高效的DNA组装，作为功能性DNA的阴性对照，作为条形码，或潜在地作为间隔区域，以使生物部件与局部环境隔离开来。该软件使用蒙特卡罗模拟退火方法创建优化序列，随后消除与宿主基因组和常用生物部件同源的序列。最终通过使用网络消除算法确定一个正交集。可以使用基于网络的图形用户界面（GUI）或上传包含一组文本命令的文件来定义设计约束。
