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Phys. Rev. E 68, 061910 (2003) [12 pages]

Universality and Shannon entropy of codon usage

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L. Frappat1,*, C. Minichini2,†, A. Sciarrino2,3,‡, and P. Sorba4,§
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
2Dipartimento di Scienze Fisiche, Università di Napoli “Federico II,” Naples, Italy
3INFN, Sezione di Napoli, Complesso Universitario di Monte S. Angelo, Via Cintia, I-80126 Naples, Italy
4CERN, Theory Division, CH-1211 Geneva 23, Switzerland

Received 28 April 2003; published 24 December 2003

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.

© 2003 The American Physical Society

URL:
http://link.aps.org/doi/10.1103/PhysRevE.68.061910
DOI:
10.1103/PhysRevE.68.061910
PACS:
87.10.+e, 02.10.-v

*Email address: frappat@lapp.in2p3.fr

†Email address: minichini@na.infn.it

‡Email address: sciarrino@na.infn.it

§On leave of absence from LAPTH, Annecy-le-Vieux Cedex, France. Email address: sorba@lapp.in2p3.fr; sorba@cern.ch

 
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