parazitCUB: An R package to streamline the process of investigating the adaptations of parasites' codon usage bias [version 1; peer review: awaiting peer review]

Examining the intricate association between parasites and their hosts, particularly at the codon level, assumes paramount importance in comprehending evolutionary processes and forecasting the characteristics of novel parasites. While diverse metrics and statistical analyses are available to explore...

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Bibliographic Details
Published in:F1000 research 2023, Vol.12, p.1431-1431
Main Authors: Anwar, Ali Mostafa, Bayoumi, Salma, Elzalabany, Sagy, Magdeldin, Sameh, Ahmed, Amr E.
Format: Article
Language:English
Subjects:
Adaptation
Amino acids
Bias
Cluster analysis
Coadaptation
Codon Usage Bias
eng
Genes
Molecular evolution
Multivariate analysis
Mutation
Natural selection
Parasites
Software
Software Tool
Statistical analysis
Viruses
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Summary:Examining the intricate association between parasites and their hosts, particularly at the codon level, assumes paramount importance in comprehending evolutionary processes and forecasting the characteristics of novel parasites. While diverse metrics and statistical analyses are available to explore codon usage bias (CUB), there presently exists no dedicated tool for examining the co-adaptation of codon usage between parasites and hosts. Therefore, we introduce the parazitCUB R package to address this challenge in a scalable and efficient manner, as it is capable of handling extensive datasets and simultaneously analyzing of multiple parasites with optimized performance. parazitCUB enables the elucidation of parasite-host interactions and the evolutionary patterns of parasites through the implementation of various indices, cluster analysis, multivariate analysis, and data visualization techniques. The tool can be accessed at the following location: https://github.com/AliYoussef96/parazitCUB
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.143223.1