Reconstruction of Phylogenetic Relationships from Metabolic Pathways Based on the Enzyme Hierarchy and the Gene Ontology

José C. Clemente[1] (
Kenji Satou[1] (
Gabriel Valiente[2] (

[1]School of Knowledge Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
[2]Department of Software, Technical University of Catalonia, E-08034 Barcelona, Spain


There has been much interest in the structural comparison and alignment of metabolic pathways. Several techniques have been conceived to assess the similarity of metabolic pathways of different organisms. In this paper, we show that the combination of a new heuristic algorithm for the comparison of metabolic pathways together with any of three enzyme similarity measures (hierarchical, information content, and gene ontology) can be used to derive a metabolic pathway similarity measure that is suitable for reconstructing phylogenetic relationships from metabolic pathways. Experimental results on the Glycolysis pathway of 73 organisms representing the three domains of life show that our method outperforms previous techniques.

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Japanese Society for Bioinformatics