Remove restriction enzyme sites while preserving amino acids

Minimizes nucleotide substitutions while preserving translation and excluding all supplied recognition sites on both strands, including sites created by other edits.

Usage

remove_cutsite(pep, ...)

Arguments

pep

A data.frame of tiled peptides

...

Named recognition sequences containing A, C, G, and T, e.g. `BbsI="GAAGAC", EcoRI="GAATTC"`. All sites are removed together.

Value

A data.frame with synonymously recoded sequences and the number of original occurrences on either strand in one `<name>_replaced` column per site. Palindromic recognition sites are counted once per occurrence.

Examples

pep = data.frame(pep_id="p1", tiled="ATGGAAGACGAATTC")
remove_cutsite(pep, BbsI="GAAGAC", EcoRI="GAATTC")
#>   pep_id           tiled BbsI_replaced EcoRI_replaced
#> 1     p1 ATGGAGGACGAGTTC             1              1