Classification and regression tree (CART) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria

Department of Biology, Wheaton College, Norton, MA 02766, USA.
Archaea (Vancouver, B.C.) (Impact Factor: 2.71). 01/2009; 2(3):159-67. DOI: 10.1155/2008/829730
Source: PubMed


Classification and regression tree (CART) analysis was applied to genome-wide tetranucleotide frequencies (genomic signatures) of 195 archaea and bacteria. Although genomic signatures have typically been used to classify evolutionary divergence, in this study, convergent evolution was the focus. Temperature optima for most of the organisms examined could be distinguished by CART analyses of tetranucleotide frequencies. This suggests that pervasive (nonlinear) qualities of genomes may reflect certain environmental conditions (such as temperature) in which those genomes evolved. The predominant use of GAGA and AGGA as the discriminating tetramers in CART models suggests that purine-loading and codon biases of thermophiles may explain some of the results.

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Available from: Mark D. LeBlanc, Jan 06, 2014
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    • "Karlin et al. [22] reported that the tetranucleotide CTAG is extremely underrepresented and distributed in an anomalous fashion along the genome of the thermophilic microbe M. jannaschi. Applying classification and regression tree (CART) analysis to genome-wide tetranucleotide frequencies of 195 archaea and bacteria, Dyer et al. [35] reported the discriminating tetramers, the frequencies of which could differentiate between three temperature ranges, hyperthermophily, thermophily and mesophily. "
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