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Freilich Lab

NetMet Tool

NetMet is a tool for predicting metabolic performances of microorganisms and their corresponding combinations in user-defined environments. The algorithm takes as input lists of:
(i) Genome file: lists of species-specific enzymatic reactions (EC numbers)
(ii) Environment File: relevant metabolic environments

The algorithm generates as output lists of:

(i) compounds that individual species can produce in each given environment
(ii) compounds that are predicted to be produced through complementary interactions

NetMet can run on single-species or interaction mode. In 'Single-species mode' prediction of metabolic capacities are made based on individual species' network in the given environment(s). 'Interaction mode' is an extension of the single-species mode, providing a list of metabolites that are produced through exchange reactions between pair-wise combinations of given species. Such metabolites are termed 'complementary metabolites' and are defined as such that are formed by species combinations but not by the corresponding individual species.

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Instructions