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Nature Research, Nature Reviews Microbiology, 3(10), p. 191-202, 2012

DOI: 10.1038/nrmicro2717

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Computational tools for the synthetic design of biochemical pathways

Journal article published in 2012 by Marnix H. Medema, Renske Van Raaphorst ORCID, Renske van Raaphorst, Eriko Takano, Rainer Breitling ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

As the field of synthetic biology is developing, the prospects for de novo design of biosynthetic pathways are becoming more and more realistic. Hence, there is an increasing need for computational tools that can support these efforts. A range of algorithms has been developed that can be used to identify all possible metabolic pathways and their corresponding enzymatic parts. These can then be ranked according to various properties and modelled in an organism-specific context. Finally, design software can aid the biologist in the integration of a selected pathway into smartly regulated transcriptional units. Here, we review key existing tools and offer suggestions for how informatics can help to shape the future of synthetic microbiology. ?? 2012 Macmillan Publishers Limited. All rights reserved.