atgc: Assistant To Genome Compilation

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Christophe Ladroue, Sara Kalvala

University of Warwick, United Kingdom

One of the aims of synthetic biology is to reach a level of systematicity and automaticity usually found in engineering. Achieving this goal requires abstracting away the details of the actual implementation and working at a higher level. When designing their organism, the user will usually make use of “active” parts like promoters and protein-coding sequences, and ignore more “house-keeping” parts like RBS and terminators. We present atgc, a biocompiler that automatically builds viable sequences of DNA given a small set of necessary parts. With no user intervention, atgc (for Assistant To Genome Compilation): a) completes the devices by adding RBS, spacers and effective terminators, b) finds a viable arrangement of the parts and c) finds the parts’ sequences in a built-in database, populated by parts from biofab and REbase. atgc thus automatically produces a biologically-plausible sequence reflecting the original aim of the user. atgc has been designed together with experimentalists and was inspired by their workflow. It comes with a simple language which allows users to add constraints on the resulting sequence. For example, it is possible a) to add in-house parts not found in the database, b) to impose the relative positions of parts, e.g. to import constructs found in the literature and c) to add multiple cloning sites, with the restriction enzymes being automatically selected. Rather than helping the user design their custom DNA sequence, atgc offers a way to automate the whole process and thus gets closer to the overall aim of synthetic biology.