Reconstruction of phylogenetic relationships from metabolic pathways based on the enzyme hierarchy and the gene ontology.

José C. Clemente, Kenji Satou, Gabriel Valiente

Research output: Contribution to journalArticlepeer-review

25 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)45-55
Number of pages11
JournalGenome informatics. International Conference on Genome Informatics
Volume16
Issue number2
StatePublished - 2005
Externally publishedYes

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