Computational Tools for Analysis of Codon Usage in Viral Genomes and its Hosts

Abstract

Analysis of codon selection in viral genomes is an important step for comprehension of the coevolution of a virus and its hosts. In this work, we developed a computational tool to simplify the analyses of codon usage. This tool, CUV or the Codon Usage Viewer, allows users to calculate and compare codon usage between viral and bacterial species including both graphical visualization and statistical analyses. To test our tool, the codon usage of homologous genes from the bacterial virus species PhiX174, G4 e alpha3, all belonging to the Microviridae family, were examined. The viruses codon usage was then compared to that of its common host, Escherichia coli. The results showed a conservation between the species codon usage.