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Journal of Applied Genetics 44(2), 2003, pp. 235-261

Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria

Jean R. LOBRY, Daniel CHESSEL


Abstract: Starting from two datasets of codon usage in coding sequences from mesophilic and thermophilic bacteria, we used internal correspondence analysis to study the variability of codon usage within and between species, and within and between amino acids. The first dataset included 18,958,458 codons from 58,482 coding sequences from completely sequenced genomes of 25 species, along with 6,793,581 dinucleotides from 21,876 intergenic spaces. The second dataset, with partially sequenced genomes, included 97,095,873 codons from 293 bacterial species. Results were consistent between the two datasets. The trend for the amino-acid composition of thermophilic proteins was found to be under the control of a pressure at the nucleic acid level, not a selection at the protein le

Key words: amino-acid usage, codon usage, correspondence analysis, thermophiles.

Correspondence: J.R. LOBRY, Laboratoire de Biometrie, Biologie Evolutive, Centre National de la Recherche Scientifique -UMR-5558, Universite Claude Bernard - LYON I, 43 Bd 11/11/1918, F-69622 Villeurbanne Cedex, France, e-mail: lobry@biomserv.univ-lyon1.fr

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