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mt1022 / cubar

R Package for Codon Usage Bias Analysis
https://mt1022.github.io/cubar/
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Codon optimisation #7

Closed maltesemike closed 1 day ago

maltesemike commented 1 week ago

Thank you for the great package and easy to follow instructions.

I've managed to run through the tutorial with my own non-model genome now.

Is there a tool to automatically codon optimise a desired sequenced based on the optimal codons cubar calculates?

mt1022 commented 1 week ago

Currently, cubar has no option for codon optimization. Do you want to replace each codon in a CDS to the optimal synonymous one? I could consider add such a function.

However, I have to mention that each codon is optimal does not mean the whole CDS is optimal. Some non-optimal codons are used on purpose, for example, to slow elongation and allow for correct co-translational folding of the nascent peptide chain.

maltesemike commented 1 week ago

That was my plan yes. I am trying to introduce a fluorescent protein transgene into our model system and my fear is that codon usage might differ, so I was hoping to optimise it to suit our system as best as possible.

A tool to optimise codon usage would this be really useful, although I did not think about your sentiments on slowing the rate of elongation. This also makes sense. Is there a way to account for this too?

I am guessing that improving the CAI of a particular CDS to match that of the most highly expressed genes in the genome would be a good start already.

mt1022 commented 1 week ago

Hi, I added a new function called codon_optimize, which replaces each codon with its optimal counterpart. Please try it out, and any feedback would be greatly appreciated.

A tool to optimise codon usage would this be really useful, although I did not think about your sentiments on slowing the rate of elongation. This also makes sense. Is there a way to account for this too?

I am afraid that there is no simple rule to do such optimization.