Open Access

Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria

EURASIP Journal on Bioinformatics and Systems Biology20072007:61374

https://doi.org/10.1155/2007/61374

Received: 31 January 2007

Accepted: 4 June 2007

Published: 25 July 2007

Abstract

G + C composition at the third codon position (GC3) is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this correlation among different genomes. Here, we applied Shannon entropy from information theory to measure the degree of GC3 bias and that of synonymous codon usage bias of each gene. The strength of the correlation of GC3 with synonymous codon usage bias, quantified by a correlation coefficient, varied widely among bacterial genomes, ranging from 0.07 to 0.95. Previous analyses suggesting that the relationship between GC3 and synonymous codon usage bias is independent of species are thus inconsistent with the more detailed analyses obtained here for individual species.

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Authors’ Affiliations

(1)
Institute for Advanced Biosciences, Keio University

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Copyright

© Haruo Suzuki et al. 2007

This article is published under license to BioMed Central Ltd. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.