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TeselaGen / tg-oss

Teselagen Open Source modules
https://teselagen.github.io/tg-oss/
MIT License
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OVE: Display not fully-matching primers #84

Closed manulera closed 2 weeks ago

manulera commented 2 weeks ago

Hi @tnrich, hope things are going well!

I think it would be quite nice to be able to display primers that don't fully overlap with the sequence. For instance, primers that have a tail at their 3' end or some mismatches. This is how they are displayed in SnapGene:

Screenshot 2024-07-10 at 10 06 34

I am thinking that in a primer_bind feature, one could add a \sequence qualifier with the primer sequence, and use that for the display.

The top case (assuming no mistmaches) is the easiest, because it would be just adding a tail behind the feature. I don't think it's necessary that the tail length is proportional, nor that it includes the sequence. If it's short maybe?

The other one is a bit more tricky, since it would be nice to position the insertions / changes on the right position of the sequence. It could be done with a * symbol or with the actual letters, but that would be a bit more complicated if there are insertions, etc.

I don't know how feasible/hard this is, but if you think it makes sense and you point me to the place in the library like last time, I can give it a go.

tnrich commented 2 weeks ago

@manulera I believe this is already implemented:

image

See here - https://teselagen.github.io/tg-oss/ove/#/Editor?searchInput=primer&allowPrimerBasesToBeEdited=true

Lemme know if that is what you're looking for..

manulera commented 2 weeks ago

Oh! Amazing! Thanks

manulera commented 2 weeks ago

Got it working, thank you!