The mutate function designs the necessary set of primers for the desired mutations. An example is given in the vignette at https://github.com/ipb-halle/GoldenMutagenesis/blob/master/vignettes/Point_Mutagenesis.md

mutate_spm(
input_sequence,
prefix = "TT",
restriction_enzyme = "GGTCTC",
suffix = "A",
vector = c("AATG", "AAGC"),
replacements,
replacement_range = 2,
binding_min_length = 4,
binding_max_length = 9,
target_temp = 60,
cuf = "e_coli_316407.csv",
fragment_min_size = 100
)

## Arguments

input_sequence The sequence which should be modified. This is an object of type character containing the sequence. Additional nucleobases in 5' position of the recognition site [default: TT] Recognition site sequence of the respective restriction enzyme [default: GGTCTC] Spacer nucleotides matching the cleavage pattern of the enzyme [default: A] Four basepair overhangs complementary to the created overhangs in the acceptor vector [default: c("AATG", "AAGC")] The desired substitutions Maximum distance in amino acid residues between two randomization sites to be incoporated into a single primer (reverse, end of the fragment) - has a cascading effect for following mutations [default: 2] The minimal threshold value of the length of the template binding sequence in amino acid residues [default: 4] Maximal length of the binding sequence in amino acid residues [default: 9] Melting temperature of the binding sequence in print('\u00B0')C [default: 60] The Codon Usage Table which is being used to select the codon for an exchanged amino acid. [default: e_coli_316407.csv] Minimal size of a generated gene fragment in base pairs [default 100]

## Value

An object of class Primerset with the designed Primers.

## Examples

#Load the setup of the Point Mutation vignette and design the primers
data(Point_Mutagenesis_BbsI_setup)
primers<-mutate_spm(input_sequence, prefix="TT", restriction_enzyme = recognition_site_bbsi,
suffix = "AA", vector=c("CTCA", "CTCG"), replacements = mutations, binding_min_length=4 ,
binding_max_length=9, target_temp=60, cuf=cuf)