TBI-Preprint 05-04-003
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Titel:
Algebraic Comparison of Metabolic Networks,
Phylogenetic Inference, and Metabolic Innovation
Author(s):
Christian Forst,
Christoph Flamm,
Ivo L. Hofacker,
Peter F. Stadler
Submitted to:
BMC Bioinformatics
Abstract:
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 Pyrococci, as well as obligate
intracellular pathogens.
Keywords:
Set algebra,
metabolic networks,
phylogeny,
Pyrococci,
intracellular pathogens
Alternative Numbers:
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Last modified: 2005-10-31 01:31:41 ivo