Several biosynthetic routes are often discovered when screening for ways of connecting the chemical target to the chassis organism through retrosynthesis. The number of alternative pathways can be very high. Pathway enumeration techniques allow determining the alternatives in a systematic way. In this chapter, we will introduce elementary flux mode analysis as one of the most successful approaches for pathway enumeration. Those enumerated pathways need to be ranked in order to select best candidate pathways to engineer. Pathway selection is a multiobjective optimization problem. Different criteria can be used for pathway selection, among others we will discuss here main factors due to enzyme performance, production capabilities and intermediate metabolite toxicity.
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- A proof-of-concept of the application of different approaches to pathway selection and ranking appeared in the report of a recent pressure test for synthetic biology biofoundries:Google Scholar
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