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Related Experiment Video

Updated: Jun 18, 2026

Purification of Viral DNA for the Identification of Associated Viral and Cellular Proteins
08:26

Purification of Viral DNA for the Identification of Associated Viral and Cellular Proteins

Published on: August 31, 2017

A detailed comparative analysis on the overall codon usage pattern in herpesviruses.

Sourav Roychoudhury1, Debaprasad Mukherjee

  • 1School of Information Technology, Bengal Engineering and Science University, Shibpur, Howrah 711103, West Bengal, India. src_4u@yahoo.co.in

Virus Research
|December 9, 2009
PubMed
Summary

Herpesviruses show weakly biased codon usage, primarily influenced by GC content, indicating mutational bias dominates translational selection. Six specific codons are frequently preferred across most herpesviral genes.

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Last Updated: Jun 18, 2026

Purification of Viral DNA for the Identification of Associated Viral and Cellular Proteins
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Detection of the Genome and Transcripts of a Persistent DNA Virus in Neuronal Tissues by Fluorescent In situ Hybridization Combined with Immunostaining
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Quantitative Fluorescence In Situ Hybridization (FISH) and Immunofluorescence (IF) of Specific Gene Products in KSHV-Infected Cells
06:21

Quantitative Fluorescence In Situ Hybridization (FISH) and Immunofluorescence (IF) of Specific Gene Products in KSHV-Infected Cells

Published on: August 27, 2019

Area of Science:

  • Genomics
  • Virology
  • Bioinformatics

Background:

  • Herpesviruses infect diverse hosts, with some explored as gene therapy vectors.
  • No prior studies comprehensively analyzed herpesvirus total codon usage patterns.

Purpose of the Study:

  • To investigate synonymous codon usage patterns in herpesviruses.
  • To identify factors influencing codon bias and evolutionary implications.

Main Methods:

  • Multivariate statistical analyses applied to 4875 open reading frames (ORFs) from 49 complete herpesvirus genomes.
  • Correspondence analysis, cluster analysis, and codon adaptation index (CAI) were employed.

Main Results:

  • A general trend of weak codon usage bias observed, with GC content and GC3 (GC content at the 3rd base position) as key determinants.
  • Mutational bias appears to be the dominant force over translational selection in herpesviruses.
  • Six codons (CUG, CAC, CAG, AAC, GUG, GAC) were frequently preferred; gene length also influenced patterns.
  • Cluster analysis showed clade-specific similarities in codon usage, with exceptions.
  • Phylogenetic analysis suggested codon usage is not directly linked to species evolution.

Conclusions:

  • Herpesvirus codon usage is predominantly shaped by mutational biases, particularly GC content.
  • Specific codons are favored across herpesviruses, but variations exist between clades.
  • Codon usage patterns do not strictly correlate with herpesvirus evolutionary history.