Starting with the set of KEGG or MicroCyc metabolic pathways predicted for each genome integrated in the PkGDB database, this method compares the metabolic content of the selected bacterial genomes.
This comparison is based on the computation of a 'pathway completion' value i.e, the number of reactions for pathway x in a given organism/total number of reactions in the same pathway x defined in the
MetaCyc or KEGG databases. To get an overview of the way compared genomes are clustered according to their metabolic capabilities, the MeV tool (http://www.tm4.org/mev/) has been integrated to this functionality:
it takes the result comparisons as input and performs a hierarchical clustering using the pathway completion values.