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Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Dec;68(6 Pt 1):061910. Epub 2003 Dec 24.

Universality and Shannon entropy of codon usage.

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  • 1Laboratoire d'Annecy-le-Vieux de Physique Théorique LAPTH, CNRS, UMR 5108 associée à l'Université de Savoie, Boîte Postale 110, F-74941 Annecy-le-Vieux Cedex, France. frappat@lapp.in2p3.fr


The distribution functions of codon usage probabilities, computed over all the available GenBank data for 40 eukaryotic biological species and five chloroplasts, are best fitted by the sum of a constant, an exponential, and a linear function in the rank of usage. For mitochondria the analysis is not conclusive. These functions are characterized by parameters that strongly depend on the total guanine and cytosine (GC) content of the coding regions of biological species. It is predicted that the codon usage is the same in all exonic genes with the same GC content. The Shannon entropy for codons, also strongly dependent on the exonic GC content, is computed.

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