Universality and Shannon entropy of codon usage

The distribution functions of the codon usage probabilities, computed over all the available GenBank data, for 40 eukaryotic biological species and 5 chloroplasts, do not follow a Zipf law, but are best fitted by the sum of a constant, an exponential and a linear function in the rank of usage. For m...

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Detalles Bibliográficos
Autores principales: Frappat, L, Minichini, C, Sciarrino, A, Sorba, Paul
Lenguaje:eng
Publicado: 2003
Materias:
Condensed Matter
Acceso en línea:http://cds.cern.ch/record/614232
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author Frappat, L
Minichini, C
Sciarrino, A
Sorba, Paul
author_facet Frappat, L
Minichini, C
Sciarrino, A
Sorba, Paul
author_sort Frappat, L
collection CERN
description The distribution functions of the codon usage probabilities, computed over all the available GenBank data, for 40 eukaryotic biological species and 5 chloroplasts, do not follow a Zipf law, but are best fitted by the sum of a constant, an exponential and a linear function in the rank of usage. For mitochondriae the analysis is not conclusive. A quantum-mechanics-inspired model is proposed to describe the observed behaviour. These functions are characterized by parameters that strongly depend on the total 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 depending on the exonic GC content, is computed.
id cern-614232
institution Organización Europea para la Investigación Nuclear
language eng
publishDate 2003
record_format invenio
spelling cern-6142322019-09-30T06:29:59Zhttp://cds.cern.ch/record/614232engFrappat, LMinichini, CSciarrino, ASorba, PaulUniversality and Shannon entropy of codon usageCondensed MatterThe distribution functions of the codon usage probabilities, computed over all the available GenBank data, for 40 eukaryotic biological species and 5 chloroplasts, do not follow a Zipf law, but are best fitted by the sum of a constant, an exponential and a linear function in the rank of usage. For mitochondriae the analysis is not conclusive. A quantum-mechanics-inspired model is proposed to describe the observed behaviour. These functions are characterized by parameters that strongly depend on the total 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 depending on the exonic GC content, is computed.cond-mat/0304577CERN-TH-2003-094DSF-2003-10LAPP-TH-968oai:cds.cern.ch:6142322003-04-25
spellingShingle Condensed Matter
Frappat, L
Minichini, C
Sciarrino, A
Sorba, Paul
Universality and Shannon entropy of codon usage
title Universality and Shannon entropy of codon usage
title_full Universality and Shannon entropy of codon usage
title_fullStr Universality and Shannon entropy of codon usage
title_full_unstemmed Universality and Shannon entropy of codon usage
title_short Universality and Shannon entropy of codon usage
title_sort universality and shannon entropy of codon usage
topic Condensed Matter
url http://cds.cern.ch/record/614232
work_keys_str_mv AT frappatl universalityandshannonentropyofcodonusage
AT minichinic universalityandshannonentropyofcodonusage
AT sciarrinoa universalityandshannonentropyofcodonusage
AT sorbapaul universalityandshannonentropyofcodonusage

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