I've got a DNA sequence that I'd like to make synonymous mutations throughout, thereby preserving the amino acid sequence. Does anyone know of a tool to achieve this
There seems to be a bioconductor package named
synmut which does just that.
Apparently, it can take codon usage into account when generating synonymous mutations.
Copy pasting an example that matches your use case from the official doc:
library("SynMut") filepath.fasta <- system.file("extdata", "example.fasta", package = "SynMut") filepath.csv <- system.file("extdata", "target_regions.csv", package = "SynMut") region <- read.csv(filepath.csv) rgd.seq <- input_seq(filepath.fasta, region) mut.seq <- codon_random(rgd.seq, keep = TRUE) Biostrings::writeXStringSet(get_dna(mut.seq), "rgd.fasta")
Additionally, you may also optimize the codon usage to match your species with ~match_codon_usage or one of the other options.
A web interface is also provided at EGF CUBA (Collection of Useful Biological Apps): Sculpt a Sequence
Disclaimer: I'm the current maintainer of DNA Chisel