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Direct comparison of the structure of metabolic networks can circumvent these problems.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>We demonstrate that metabolic networks contain valuable phylogenetic information by comparing phylogenies obtained from network comparisons with 16S RNA phylogenies. The algebraic approach to metabolic networks is suitable to study metabolic innovations in two sets of organisms, free living microbes and <jats:italic>Pyrococci<\/jats:italic>, as well as obligate intracellular pathogens.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-7-67","type":"journal-article","created":{"date-parts":[[2006,2,17]],"date-time":"2006-02-17T07:45:25Z","timestamp":1140162325000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":34,"title":["Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation"],"prefix":"10.1186","volume":"7","author":[{"given":"Christian V","family":"Forst","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Flamm","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivo L","family":"Hofacker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter F","family":"Stadler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2006,2,14]]},"reference":[{"key":"806_CR1","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/1471-2180-5-8","volume":"5","author":"SA Becker","year":"2005","unstructured":"Becker SA, Palsson BO: Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. 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