Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 05-017

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Algebraic Comparison of Metabolic Networks, Phylogenetic Inference, and Metabolic Innovation

Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler


Metabolic networks are naturally represented as directed hypergraphs in such a way that metabolites are nodes and enzyme-catalyzed reactions form (hyper)edges. The familiar operations from set algebra (union, intersection, and difference) form a natural basis for both the pairwise comparison of networks and identification of distinct metabolic features of a set of algorithms. We report here on an implementation of this approach and its application to the procaryotes. We demonstrate that metabolic networks contain valuable phylogenetic information by comparing phylogenies obtained from network comparisons with 16S RNA phylogenies. We then used the same software to study metabolic innovations in two sets of organisms, free living microbes and \emph{Pyrococci}, as well as obligate intracellular pathogens.

Keywords: Set algebra, metabolic networks, phylogeny, Pyrococci, intracellular pathogens

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