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Oxford University Press (OUP), Bioinformatics, 7(27), p. 973-979

DOI: 10.1093/bioinformatics/btr048

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Model annotation for synthetic biology: automating model to nucleotide sequence conversion

Journal article published in 2011 by Goksel Misirli, Jennifer S. Hallinan, Tommy Yu, James R. Lawson, Sarala M. Wimalaratne ORCID, Michael T. Cooling ORCID, Anil Wipat
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Motivation: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the assembly of models of individual parts such as promoters, ribosome binding sites and coding sequences. These low level models are combined to produce a dynamic model of a larger device that exhibits a desired behaviour. The larger model then acts as a blueprint for physical implementation at the DNA level. However, the conversion of models of complex genetic circuits into DNA sequences is a non-trivial undertaking due to the complexity of mapping the model parts to their physical manifestation. Automating this process is further hampered by the lack of computationally tractable information in most models.