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. 2019 Dec 23:8:2137.
doi: 10.12688/f1000research.21763.1. eCollection 2019.

vhcub: Virus-host codon usage co-adaptation analysis

Ali Mostafa Anwar  1 , Mohamed Soudy  2 , Radwa Mohamed  1
Affiliations

vhcub: Virus-host codon usage co-adaptation analysis

Ali Mostafa Anwar et al. F1000Res. .

Abstract

Viruses show noticeable evolution to adapt and reproduce within their hosts. Theoretically, patterns and factors that affect the codon usage of viruses should reflect evolutionary changes that allow them to optimize their codon usage to their hosts. Some software tools can analyze the codon usage of organisms; however, their performance has room for improvement, as these tools do not focus on examining the codon usage co-adaptation between viruses and their hosts. This paper describes the vhcub R package, which is a crucial tool used to analyze the co-adaptation of codon usage between a virus and its host, with several implementations of indices and plots. The tool is available from: https://cran.r-project.org/web/packages/vhcub/.

Keywords: Adaptation; Codon Usage Bias; Evolution; Natural selection; R; RStudio; Viruses.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. vhcub workflow, to analyze virus-host codon usage co-adaptation.
The white boxes represent the input fasta files. The red boxes represent three main analysis, each with different measures (the blue boxes), and the orange boxes represent ENc-GC3 plot and PR2-plot.
Figure 2.
Figure 2.. ENc-GC3 plot showing the values of the ENc versus the GC3 content for the virus (Escherichia virus T4) CDS, the solid red line represents the expected ENc values if the codon bias is affected by GC3s only.
Figure 3.
Figure 3.. PR2-plot showing CDS of the virus (Escherichia virus T4), plotted based on their GC bias [G3/(G3 + C3)] and AT bias [A3/(A3 + T3)] in the third codon position, the two solid red lines represent both coordinates (ordinate and abscissa) equal to 0.5, where A = T and G = C.
See this image and copyright information in PMC

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