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Nucleic Acids Res. 2009 Jan;37(Database issue):D531-8. doi: 10.1093/nar/gkn826. Epub 2008 Oct 25.

metaTIGER: a metabolic evolution resource.

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  • 1Institute of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, W. Yorks, LS2 9JT, UK.

Abstract

Metabolic networks are a subject that has received much attention, but existing web resources do not include extensive phylogenetic information. Phylogenomic approaches (phylogenetics on a genomic scale) have been shown to be effective in the study of evolution and processes like horizontal gene transfer (HGT). To address the lack of phylogenomic information relating to eukaryotic metabolism, metaTIGER (www.bioinformatics.leeds.ac.uk/metatiger) has been created, using genomic information from 121 eukaryotes and 404 prokaryotes and sensitive sequence search techniques to predict the presence of metabolic enzymes. These enzyme sequences were used to create a comprehensive database of 2257 maximum-likelihood phylogenetic trees, some containing over 500 organisms. The trees can be viewed using iTOL, an advanced interactive tree viewer, enabling straightforward interpretation of large trees. Complex high-throughput tree analysis is also available through user-defined queries, allowing the rapid identification of trees of interest, e.g. containing putative HGT events. metaTIGER also provides novel and easy-to-use facilities for viewing and comparing the metabolic networks in different organisms via highlighted pathway images and tables. metaTIGER is demonstrated through evolutionary analysis of Plasmodium, including identification of genes horizontally transferred from chlamydia.

PMID:
18953037
[PubMed - indexed for MEDLINE]
PMCID:
PMC2686446
Free PMC Article

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