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Nucleic Acids Research, 2001, Vol. 29, No. 7 1608-1615
© 2001 Oxford University Press

Identification of thermophilic species by the amino acid compositions deduced from their genomes

David P. Kreil1,2,* and Christos A. Ouzounis2

1University of Cambridge and 2European Bioinformatics Institute, Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK

The global amino acid compositions as deduced from the complete genomic sequences of six thermophilic archaea, two thermophilic bacteria, 17 mesophilic bacteria and two eukaryotic species were analysed by hierarchical clustering and principal components analysis. Both methods showed an influence of several factors on amino acid composition. Although GC content has a dominant effect, thermophilic species can be identified by their global amino acid compositions alone. This study presents a careful statistical analysis of factors that affect amino acid composition and also yielded specific features of the average amino acid composition of thermophilic species. Moreover, we introduce the first example of a ‘compositional tree’ of species that takes into account not only homologous proteins, but also proteins unique to particular species. We expect this simple yet novel approach to be a useful additional tool for the study of phylogeny at the genome level.

* To whom correspondence should be addressed. Tel: +44 1223 494 663; Fax: +44 1223 494 468; Email: kreil{at}ebi.ac.uk


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