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Predicting genes for orphan metabolic activities using phylogenetic profiles

Lifeng Chen and Dennis Vitkup*

Author Affiliations

Center for Computational Biology and Bioinformatics and Department of Biomedical Informatics, Columbia University, St Nicholas Avenue, Irving Cancer Research Center, New York, NY 10032, USA

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Genome Biology 2006, 7:R17  doi:10.1186/gb-2006-7-2-r17

Published: 15 February 2006


Homology-based methods fail to assign genes to many metabolic activities present in sequenced organisms. To suggest genes for these orphan activities we developed a novel method that efficiently combines local structure of a metabolic network with phylogenetic profiles. We validated our method using known metabolic genes in Saccharomyces cerevisiae and Escherichia coli. We show that our method should be easily transferable to other organisms, and that it is robust to errors in incomplete metabolic networks.