Journal of
Bioinformatics and Sequence Analysis

  • Abbreviation: J. Bioinform. Seq. Anal.
  • Language: English
  • ISSN: 2141-2464
  • DOI: 10.5897/JBSA
  • Start Year: 2009
  • Published Articles: 43

Full Length Research Paper

Analysis of factors affecting codon usage bias in human papillomavirus

Takaaki Kamatani
  • Takaaki Kamatani
  • Department of Oral and Maxillofacial Surgery, Showa University School of Dentistry, Kitasenzoku 2-1-1, Ota City, Tokyo, 145-8515, Japan.
  • Google Scholar
Tatsuo Shirota
  • Tatsuo Shirota
  • Department of Oral and Maxillofacial Surgery, Showa University School of Dentistry, Kitasenzoku 2-1-1, Ota City, Tokyo, 145-8515, Japan.
  • Google Scholar


  •  Received: 08 April 2017
  •  Accepted: 29 December 2017
  •  Published: 31 January 2018

Abstract

Indices of codon usage pattern of human papillomavirus (HPV) were analyzed to understand the key determinants of synonymous codon usage in the HPV genome. The complete sequences of 39 HPV genomes were downloaded from the website of the National Center for Biotechnology Information. The relative synonymous codon usage values, effective number of codons, GC content, percentage of GCs at the third position of synonymous codons (GC3s), codon adaptation index, hydrophobicity, aromaticity of conceptually translated gene products were calculated using the Codon W 1.4.2 program. HPV preferentially used codons ending with A/U. By comparing relative synonymous codon usage of the HPV genome and human genome, the codon usage of HPV was almost entirely different from that of humans. Statistical significant of the separation between codons ending with A/U and G/C on the first axis was shown by the principal component analysis. The greater number of the effective number of codon values against the value of GC3s was below the expected values. The correlation between effective number of codon values and both aromaticity and hydrophobicity showed significant high negative correlation. These results showed that composition constraint is likely the key element for codon usage in the HPV genome.

 

Key words: Principal component analysis, composition constraints, papilloma virus, codon usage.