domesticate: Domestication of the input sequence

In ipb-halle/GoldenMutagenesis: A tool to calculate and validate primers for Golden Gate Cloning

Description

The domesticate function checks for internal cleavage sites. If corresponding sites are present silent mutations are introduced to destroy the recognition sites. The functions returns a list containing the position of the choosen amino acid residue for silent mutation.

Usage

domesticate(
  input_sequence,
  restriction_enzyme = "GGTCTC",
  cuf = "e_coli_316407.csv"
)

Arguments

input_sequence	The sequence which should be modified. This is an object of type character containing the sequence.
restriction_enzyme	Recognition site sequence of the respective restriction enzyme [default: GGTCTC]
cuf	The Codon Usage Table which is being used to select the codon for an exchanged amino acid (and in this case to select the codon which shoulb be replaced). [default: e_coli_316407.csv]

Value

A list with replacments: Each element has a vector with the codon number at the first slot and the amino acid of this position at the second slot.

Examples

#Load the setup of the Point Mutation vignette and run the domestication
data(Point_Mutagenesis_BbsI_setup)
domesticate(input_sequence, restriction_enzyme=recognition_site_bbsi, cuf=cuf)

ipb-halle/GoldenMutagenesis documentation built on Sept. 1, 2020, 3:24 p.m.