Variation in the correlation of G + C composition with synonymous codon usage bias among bacteria

Haruo Suzuki, Rintaro Saito, Masaru Tomita

Research output: Contribution to journalArticle

5 Citations (Scopus)

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.

Original languageEnglish
Article number61374
JournalEurasip Journal on Bioinformatics and Systems Biology
Volume2007
DOIs
Publication statusPublished - 2007

Fingerprint

Base Composition
Codon
Bacteria
Genes
Chemical analysis
Information theory
Genome
Information Theory
Bacterial Genomes
Entropy
Shannon Entropy
Correlation coefficient
Inconsistent
Gene

ASJC Scopus subject areas

  • Medicine(all)
  • Computer Science(all)
  • Signal Processing
  • Statistics and Probability
  • General

Cite this

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