The CPT wanted to include a Codon Optimisation tool in Galaxy, but none of the existing ones are open source or willing to release their source. So, we wrote our own! We were able to add some extra, nice features as a result of this.
We have an extensive library of bacterial codon usage data thanks to Kazusa.or.jp published codon usage tables for all of GenBank.
The new tool takes a single fasta file and optionally a bed file of regions. If you have a large sequence you wish to optimise, but want to “mask” some regions which you want optimised, you can use this selector to do it. Bed datasets are very simple files, with just a fasta ID of the parent sequence, and a start and end:
pRE 1 210
The above example would specify that only the region from 1..210 should be optimised. If you don’t specify which regions you wish to optimise, the tool will optimise the entire sequence.