TY - JOUR
T1 - Variation in the correlation of G + C composition with synonymous codon usage bias among bacteria
AU - Suzuki, Haruo
AU - Saito, Rintaro
AU - Tomita, Masaru
N1 - Copyright:
Copyright 2008 Elsevier B.V., All rights reserved.
PY - 2007
Y1 - 2007
N2 - 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.
AB - 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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U2 - 10.1155/2007/61374
DO - 10.1155/2007/61374
M3 - Article
C2 - 18350114
AN - SCOPUS:36248947407
VL - 2007
JO - Eurasip Journal on Bioinformatics and Systems Biology
JF - Eurasip Journal on Bioinformatics and Systems Biology
SN - 1687-4145
M1 - 61374
ER -