What to do when homology arms don't match genome sequence?

[manulera]

This happens in the MYTK MoClo kit, where the sequence of the homology arms of 500bp does not exactly match that of the genome, having a few mistmaches. What to do in a case like this? Include Ns?

[manulera]

Causes something like this: manulera/OpenCloning_frontend#241

[dgruano]

To me, it would make sense to add the Ns (or any of the other IUPAC symbols. We could validate them later with sequencing results, like we would do for this issue.

Additionally, we could:

1. Add a feature named "unknown recombination site"
2. Label the construct as "unfinished" or "missing information" so the users pay attention

[manulera]

Yes, I agree that it makes sense to use those symbols. The issue is that sometimes there will be gaps, and that is not really supported by the letter notation (would have to be something like N or -.

Also, we would have to decide what to do with the annotation present in the plasmid or locus and how to transmit it.

I would say that this is something to think about but not prioritary to fix, since at least for the time being we can prioritise the sequence of the insert.