vhcub

vhcub analyzes codon usage co-adaptation between viruses and their host organisms to quantify codon usage bias and similarity and to visualize related patterns.

Key Features:

• Effective Number of Codons (ENc): Measures the degree of codon usage bias within genes.
• Codon Adaptation Index (CAI): Assesses how well a gene's codon usage matches the preferred codon usage of highly expressed host genes.
• Relative Codon Deoptimization Index (RCDI): Evaluates the extent to which viral codons are deoptimized relative to host codon usage.
• Similarity Index (SiD): Compares similarity between viral and host codon usage patterns.
• Synonymous Codon Usage Orderliness (SCUO): Quantifies the orderliness of synonymous codon usage within a gene.
• Relative Synonymous Codon Usage (RSCU): Provides relative frequencies of synonymous codons.
• Visualization (ENc-GC3 and PR2 plots): Generates ENc-GC3 plots to relate ENc to GC content at the third codon position and PR2 plots to examine factors influencing codon usage bias, using ggplot2.

Scientific Applications:

• Viral evolution analyses: Infer evolutionary strategies by assessing how viruses adapt codon usage to host cellular machinery.
• Host adaptation assessment: Quantify co-adaptation between viral genomes and host codon usage patterns.
• Antiviral target identification: Highlight codon usage adaptations in viral genomes that may inform targets for antiviral strategies.

Methodology:

Computes codon usage indices (ENc, CAI, RCDI, SiD, SCUO, RSCU) and generates ENc-GC3 and PR2 plots using ggplot2, integrating these indices via statistical methodologies.