Analysis of synonymous codon usage patterns in duck hepatitis A virus: a comparison on the roles of mutual pressure and natural selection.

ABSTRACT: Codon usage patterns of duck hepatitis A virus (HAV) were studied in the present study. The major trends of codon usage patterns were analyzed using principal component analysis on the basis of the relative synonymous codon usage values. Correlation analysis was utilized to reveal the associations of the first two major axes of PCA and nucleotide- or amino acid-relevant indices. Our results showed that compositional constraint and/or mutational pressure are major factors influencing codon usage bias patterns of HAV. However, the influence of natural selection is also prevalent, as indicated by strongly significant correlations between the hydrophobicity, aromaticity, aliphaticity and ionization and the first axis of PCA. Also, ionization could characterize the second axis of PCA. At last,

SUBMITTER: Chen Y 

PROVIDER: S-EPMC4188199 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature