The falling cost of DNA synthesis and the increasing breadth of genomic datasets have prompted the question: Is it possible to design and build a working genome from scratch? The goal of our Saccharomyces cerevisiae v2.0 project is the complete synthesis of a redesigned genome for baker's yeast. However, all large synthetic projects, including ours, currently face several logistical stumbling blocks: One, manipulations that are simple enough to be accomplished by manual editing at the gene-scale become infeasible if done by hand at the genome-scale. Two, as a project progresses there will be many versions of the synthetic genome, which must be carefully annotated and tracked to allow a “roll-back” in case of lethal modifications. Three, the efficiency of chemical synthesis of DNA does not yet permit direct synthesis of an entire chromosome, although it is now feasible to synthesize multikilobase pieces of DNA that can be combined into larger molecules. Finally, the biggest problem is that there are no computational tools to address any of these issues on the scale required for a synthetic genome project. To solve this, we created GeneDesign, BioStudio, and CloneQC – open-source software for computer-assisted design and assembly of synthetic DNA molecules. Together they form a comprehensive package: GeneDesign and Biostudio can modify nucleotide sequences automatically and manually at multiple resolutions and generate oligonucleotides for physical assembly of the designed sequence; BioStudio provides workflow management for all stages of the physical assembly process; and CloneQC offers automated analysis of the physical products of synthesis. With these tools, we have accomplished the design of several yeast chromosomes as well as the assembly of many large pieces of the same.
