Comparative Analysis of Non-Synonymous and Synonymous Substitution of Capsid Proteins of Human Herpes Virus
- *Corresponding Author:
- Vipan Kumar Sohpal
Department of Chemical & Biotechnology
Beant College of Engineering & Technology
Gurdaspur, Punjab, India
E-mail: [email protected]
Received Date: June 22, 2012; Accepted Date: August 07, 2012; Published Date: August 09, 2012
Citation: Vipan Kumar S, Apurba D, Amarpal S (2012) Comparative Analysis of Non-Synonymous and Synonymous Substitution of Capsid Proteins of Human Herpes Virus. J Proteomics Bioinform 5: 172-176. doi: 10.4172/jpb.1000231
Copyright: © 2012 Vipan Kumar S, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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.