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Vhcub: Virus-host codon usage co-adaptation analysis.


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/.

SUBMITTER: Anwar AM 

PROVIDER: S-EPMC7104870 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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<i>vhcub</i>: Virus-host codon usage co-adaptation analysis.

Anwar Ali Mostafa AM   Soudy Mohamed M   Mohamed Radwa R  

F1000Research 20191223


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 <i>vhc  ...[more]

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