Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks

Raising the level of abstraction for synthetic biology
design requires
solving several challenging problems, including mapping abstract designs
to DNA sequences. In this paper we present the first formalism and
algorithms to address this problem. The key steps of this transformation
are feature matching, signal matching, and part matching. Feature matching ensures that
the mapping satisfies the regulatory relationships in the abstract
design. Signal matching ensures that the expression levels of functional
units are compatible. Finally, part matching finds a DNA part sequence
that can implement the design. Our software tool MatchMaker implements these three steps.