sscu

sscu analyzes codon usage bias in bacterial species to quantify selection on codon usage and identify optimal codons for studies of translational selection and gene expression optimization.

Key Features:

• Selective Strength Calculation: Calculates the strength of selected codon usage bias using Paul Sharp's method for comparative analysis across bacterial species.
• Translational Accuracy Inference: Infers selection for translational accuracy using Akashi's test.
• Optimal Codon Lists Calculation: Generates lists of optimal codons via functions op_highly, op_corre_CodonW, and op_corre_NCprime for downstream use in gene design and analysis.

Scientific Applications:

• Comparative Genomics: Enables analysis of codon usage patterns across species to investigate evolutionary pressures in bacterial genomes.
• Gene Expression Optimization: Identifies optimal codons to guide design of genes for improved expression in heterologous systems.
• Translational Efficiency Studies: Supports investigations into mechanisms of translational efficiency and accuracy affecting protein synthesis.

Methodology:

Implements Paul Sharp's method for selective strength, Akashi's test for translational accuracy, and functions op_highly, op_corre_CodonW, and op_corre_NCprime to compute optimal codon lists; implemented in R and distributed via Bioconductor.