Journal of Proteomics & Bioinformatics
Open Access

Abstract

Comparative Analysis of Non-Synonymous and Synonymous Substitution of Capsid Proteins of Human Herpes Virus

Vipan Kumar Sohpal, Apurba Dey and Amarpal Singh

The difference between non-synonymous (dN) to synonymous (dS) changes between sequence is computed to assay the direction of evolution. In this paper we compare closely related strains HHV species, codon-by-codon using maximum likelihood analysis and the divergence time of the two sequences. We demonstrate that a substitution model provides evolution hypothesis when comparing closely related species. The effect of transition/transversion ratio and Fischer exact test are on dN-dS (p-distance), and the problems associated with these concepts for HHV, are also discussed. We applied methods on sequence capsid protein of the HHV-1 and HHV-2 for detailed analyses of capsid structures provides the best evidence for an evolution. We conclude that substitution models, dN-dS, divergence time and transition/transversion have critical role to study the evolution.