title: Computational tools for the synthetic design of biochemical pathways.
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.
authors.affiliation: Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
authors.forename: Marnix H
authors.initials: MH
authors.lastname: Medema
authors.forename: Renske
authors.initials: R
authors.lastname: van Raaphorst
authors.forename: Eriko
authors.initials: E
authors.lastname: Takano
authors.forename: Rainer
authors.initials: R
authors.lastname: Breitling
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D053858:Metabolic Networks and Pathways; D008828:Microbiological Techniques; D012984:Software; D058615:Synthetic Biology / Q000379:methods*