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Computational and Mathematical Methods in Medicine
Volume 2013, Article ID 848123, 10 pages
http://dx.doi.org/10.1155/2013/848123
Research Article

Complex Codon Usage Pattern and Compositional Features of Retroviruses

1School of Information Technology, Bengal Engineering and Science University, Shibpur, Howrah, West Bengal 711103, India
2School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
3Department of Information Technology, Dr. B.C. Roy Engineering College, West Bengal University of Technology, Durgapur, West Bengal 713206, India

Received 30 May 2013; Revised 5 September 2013; Accepted 7 September 2013

Academic Editor: Kazuhisa Nishizawa

Copyright © 2013 Sourav RoyChoudhury and Debaprasad Mukherjee. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Retroviruses infect a wide range of organisms including humans. Among them, HIV-1, which causes AIDS, has now become a major threat for world health. Some of these viruses are also potential gene transfer vectors. In this study, the patterns of synonymous codon usage in retroviruses have been studied through multivariate statistical methods on ORFs sequences from the available 56 retroviruses. The principal determinant for evolution of the codon usage pattern in retroviruses seemed to be the compositional constraints, while selection for translation of the viral genes plays a secondary role. This was further supported by multivariate analysis on relative synonymous codon usage. Thus, it seems that mutational bias might have dominated role over translational selection in shaping the codon usage of retroviruses. Codon adaptation index was used to identify translationally optimal codons among genes from retroviruses. The comparative analysis of the preferred and optimal codons among different retroviral groups revealed that four codons GAA, AAA, AGA, and GGA were significantly more frequent in most of the retroviral genes inspite of some differences. Cluster analysis also revealed that phylogenetically related groups of retroviruses have probably evolved their codon usage in a concerted manner under the influence of their nucleotide composition.