Correlation matrix for quartet codon usage

It has been argued that the sum of usage probabilities for codons, belonging to quartets, that have as third nucleotide C or A, is independent of the biological species for vertebrates. The comparison between the theoretical correlation matrix derived from these sum rules and the experimentally comp...

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Bibliographic Details
Published inPhysica A Vol. 351; no. 2; pp. 461 - 476
Main Authors Frappat, L., Sciarrino, A., Sorba, P.
Format Journal Article
LanguageEnglish
Published Elsevier B.V 15.06.2005
Elsevier
Subjects
Biological Physics
Codon usage
Condensed Matter
Correlation
Entropy
Genome
Information
Other
Physics
Correlation
Codon usage
87.10.+e
Entropy
02.10. - v
Genome
Information
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Summary:It has been argued that the sum of usage probabilities for codons, belonging to quartets, that have as third nucleotide C or A, is independent of the biological species for vertebrates. The comparison between the theoretical correlation matrix derived from these sum rules and the experimentally computed matrix for 26 species shows a satisfactory agreement. The Shannon entropy, weakly depending on the biological species, gives further support. Suppression of codons containing the dinucleotides CG or AU is put in evidence.
ISSN:0378-4371
1873-2119
0378-4371
DOI:10.1016/j.physa.2005.01.051