vhcub: Virus-host codon usage co-adaptation analysis [version 1; peer review: 2 approved]

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...

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Bibliographic Details
Published in:F1000 research 2019, Vol.8, p.2137-2137
Main Authors: Anwar, Ali Mostafa, Soudy, Mohamed, Mohamed, Radwa
Format: Article
Language:English
Subjects:
Amino acids
Bias
Coadaptation
Codon
Codon Usage
Deoxyribonucleic acid
DNA
E coli
Evolution, Molecular
Genome, Viral
Genomes
Software
Software Tool
Viruses
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Summary: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/.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.21763.1