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Identification of thermophilic species by the amino acid compositions deduced from their genomes
Open accessAbstract
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.
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Cited by
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Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B., & Bork, P. (2006) · Science · doi:10.1126/science.1123061 · Cited by 1,663
Protein and DNA Sequence Determinants of Thermophilic Adaptation
Zeldovich, K. B., Berezovsky, I. N., & Shakhnovich, E. I. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030005 · Cited by 325
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Daubin, V., Gouy, M., & Perrière, G. (2002) · Genome Research · doi:10.1101/gr.187002 · Cited by 313
Zhu, Y., Wang, G., Ni, H., Xiao, A., & Cai, H. (2014) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-013-1536-5 · Cited by 41
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Metadata
- Authors
- Kreil, D. P.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2001-04-01
- Volume
- 29
- Issue
- 7
- Pages
- 1608-1615
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2153901638
- Cited by
- 185
- References
- 0
- FWCI
- 4.02
- Type
- journal article
- Language
- en
- Open access
- green
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