evolution: Generate synonimous mutant variants

In santiago1234/iCodon: iCodon: Designing "ideal" coding (iCodon) sequences for customized expression level

Generate synonimous mutant variants

Description

Generate synonimous mutant variants

Usage

evolution(
  starting_sequence,
  sampling_distribution,
  mutation_rate = 0.3,
  n_daughters = 10
)

Arguments

starting_sequence	string, coding DNA sequence in frame
sampling_distribution	function, sample_synonimous_codon the sampling codon distribution
mutation_rate	number of positions to be mutated expressed as a percentage max = 1 (mutate all codons), min = 0 (mutate no codons). the 1st and last codon are never changed
n_daughters	int, the number of random synonimous sequences to generate at each function call

Value

function, sinonimous generator: A function that takes as input a sequence and will create sinonimous mutations in that sequence

Examples

sampling_distribution <- sample_synonimous_codon(
  sampling_codon_distribution = sampling_deoptimization
)
seq <- "ATGCCCGGGATGATGTTT"
evolution(seq, sampling_distribution)

santiago1234/iCodon documentation built on Nov. 2, 2023, 2:03 p.m.