knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "100%" )
The goal of reversetranslate
is to provide a set of R functions to assist users in reverse translating an amino acid sequence to DNA nucleotides.
You can install the development version from GitHub with:
# install.packages("devtools") devtools::install_github("greg-botwin/reversetranslate")
Users can supply their own Codon Frequency Table relevant to the organism they are most interested in simulating the reverse translation in or use one of the commonly desired options supplied. Users can also select between the following three different models of reverse translation depending on what assumptions you want to make regarding how redundant codons are chosen and your intended application.
The user may also choose to limit the inclusion of low frequency codons into the reverse translated nucleotide sequence.
The package currently maintains Codon Frequency Tables for:
Additional details on package functionality can be found by viewing the package vignette.
library(reversetranslate)
minimal_aa_seq
minimal_freq_tbl
reverse_translate(amino_acid_seq = minimal_aa_seq, codon_tbl = minimal_freq_tbl, limit = 0, model = "proportional")
This work was supported by Cedars-Sinai Precision Health.
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