Predicting genes for orphan metabolic activities using phylogenetic profiles

Genome Biology
Lifeng Chen, Dennis Vitkup

Abstract

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.

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Citations

Jun 10, 2008·Nature Biotechnology·Adam M Feist, Bernhard Ø Palsson
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Methods Mentioned

BETA
phylogenetic profiles
phylogenetic profile

Software Mentioned

BLAST
TrEMBL

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