README.md

In ec363/synonymise: Generate synonymous CDS of frequently used protein motifs, keep DNA synthesis companies happy!

synonymise

What does this package do?

Taking an input DNA coding sequence (CDS), this package allows user to generate synonymous replacements of the codons in the CDS at a selected frequency and excluding certain sets of codons. This package includes a codon table and a list of very rare (frequency of <5/1000) and rare codons (5-10 /1000). Note that codon usage is species specific though, and the provided lists are currently specific to E. coli B strains. Codon usage data is from https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=413997 where data for other species can be found.

Why would you want to do this?

Synthetic DNA designs frequently necessitate the use of recurrent sequence motifs, including protein elements such linkers, tags, localisation sequences and reporters. Automated checks by DNA synthesis companies frequently flag initial designs as being too "complex", and such complexity usually results from direct DNA level repeats. While altering DNA and RNA motifs are harder to do, protein elements may be varied on the DNA level by replacing codons with synonymous variants, without affecting the element's function. The aim of this package is to provide a way to automate this process to avoid having to do it manually. While similar tools do exist, they are often simplistic or not fit for purpose.

Unlike similar tools, the function in this package:

(a) doesn't replace stop codons or treat them as rare,

(b) rare codons can be excluded but this is optional and can be specified manually,

(c) the replacement codon is randomised so that you don't just end up using same codon for each (eg.) Alanine,

(d) the frequency of changes can be specified such that not every codon is changed.

Codons requiring replacement but that do not have a synonymous alternative, or any non-forbidden alternatives will return the original codon silently. All changed codons are returned in lower case, allowing inspection. A verbose option helps to follow the function as it is working.

Some more specifics:

The frequency parameter allows you to specify how often to edit a codon: every codon = 1, every 3 codons = 3. It is specified by the term index%%frequency == 0, ie. for frequency of 3, it will start editing on codon 3 (then every 3rd codon after).

The displacement parameter allows you to start editing on a codon other than the one provided by the frequency value alone, that is, when frequency = 3 and displacement = 0, the first edited codon will be the third codon. To start at codon 1 instead, then codon 4, etc, use frequency = 3, displacement = 1, which gets the index of the first codon to 0 (so index%%frequency will be 0).

Note

Please note that this is a tool developed for personal use, and is subject to continued improvements. However, I'd be happy if it was useful to others, and I'd welcome feedback/suggestions for its improvement.

Installation and Example Usage

Installing the package

The package is written in R and can be installed straight from GitHub:

# install.packages("devtools") # if it's not already installed
devtools::install_github("ec363/synonymise")

Example script

An example script is included to illustrate how you can use this package.

# Example script ####

library(synonymise)

# Get codon table ####
codon_table <- loadcodontable()

# Get rare codon tables (E coli B) ####
very_rare_codons_B <- loadveryrarecodons_B()
rare_codons_B <- loadrarecodons_B()

# Take CDS as string, select alternative codons for each, and paste as string: ####
# Note that results may vary due to sampling

# Replace every codon:
new1 <- synonymise(cds = "GGGAAACCCTAG", codon_table = codon_table, forbidden_codons = c(very_rare_codons_B, rare_codons_B), frequency = 1, displacement = 0)
new1
# example output: ggcaaaccgtag

# Replace every 2nd codon:
new2 <- synonymise(cds = "GGGAAACCCTAG", codon_table = codon_table, forbidden_codons = c(very_rare_codons_B, rare_codons_B), frequency = 2, displacement = 0)
new2
# example output: GGGaaaCCCtag

# Replace every 3rd codon, starting at codon3:
new3 <- synonymise(cds = "GGGAAACCCTAG", codon_table = codon_table, forbidden_codons = c(very_rare_codons_B, rare_codons_B), frequency = 3, displacement = 0)
new3
# example output: GGGAAAccaTAG

# Replace every 3rd codon, starting at codon1:
new4 <- synonymise(cds = "GGGAAACCCTAG", codon_table = codon_table, forbidden_codons = c(very_rare_codons_B, rare_codons_B), frequency = 3, displacement = 1)
new4
# example output: ggtAAACCCtag

ec363/synonymise documentation built on Aug. 9, 2020, 1:34 a.m.