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Genome scale network analysis / Avoiding connection on side compounds
age-old question in the metabolic network reconstruction : how identify in the most efficient way the side compounds in each reaction (in order to avoid to connect reactions between them on these side compounds)?
I generally use the known metabolic pathways, as they generally define primary and side compounds in function of the pathway backbone, but with this method I loose all the reactions that are not (yet) described in a metabolic pathway available in public database.
Any thoughts?