codon_optimize {cubar}

Optimize codons

Description

codon_optimize takes a coding sequence (without stop codon) and replace each codon to the corresponding synonymous optimal codon.

Usage

codon_optimize(seq, optimal_codons, gcid = "1")

Arguments

seq

DNAString, or an object that can be coerced to a DNAString

optimal_codons

table optimze codons as generated by est_optimal_codons

gcid

genetic code id, default is '1' (standard genetic code)

Value

a DNAString of the optimized coding sequence

Examples

optimal_codons <- est_optimal_codons(yeast_cds)
seq <- 'ATGCTACGA'
codon_optimize(seq, optimal_codons)