Constraint-based genetic compilation

Abstract

Synthetic biology aims at facilitating the design of new organisms via the standardization of biological parts and following engineering principles. We present atgc (Assistant To Genetic Compilation), a software tool that automatically builds a functional sequence of DNA from a minimal set of requirements. Through a simple language, the user provides in-house knowledge about their construct (e.g. relative placement of parts, number of restriction enzymes). atgc combines information from established biology, user knowledge and bioinformatics databases, and maps the problem to a constraint satisfaction setting. The solution is a functional DNA sequence ready to be assembled and transferred to a target organism.