Comparison of Metabolic Pathways by Considering Potential Fluxes

Comparison of metabolic pathways is useful in phylogenetic analysis and for understanding metabolic functions when studying diseases and in drugs engineering. In the literature many techniques have been proposed to compare metabolic pathways, but most of them focus on structural aspects, while behavioural or functional aspects are generally not considered. In this paper we propose a new method for comparing metabolic pathways of different organisms based on a similarity measure which considers both homology of reactions and functional aspects of the pathways. The latter are captured by relying on a Petri net representation of the pathways and comparing the corresponding T-invariant bases, which represent potential fluxes in the nets. The approach is implemented in a prototype tool, CoMeta, which allows us to test and validate our proposal. Some experiments with CoMeta are presented.