manulera
Add checking primers
Allow to associate checking primers with a sequence,
should be possible to select a region to create the checking primers
Related to this:
OpenCloning can currently recognize already existing features and primers from an imported file (e.g. .dna SnapGene files). I was doing a PCR from a SnapGene file and I wondered if I could use the primers already annotated in the file to do such PCR. To my understanding, I could not find a way to automatically select the recognized primers to be used for the PCR.
Being able to import primers via .csv/.tsv files is awesomely useful already, but could it be possible to select already-existing primers annotated in imported files to do a PCR?
Hi @mrbertp !
It should be feasible to implement and very useful indeed. Do you have an example file that can be shared for testing? I can work on it during our upcoming Hackathon.
Cheers,
Daniel
Here you have. It is a gene (ORF and flanking 1000bp) with two primers.
Thank you.
This would be nice, but I have a lot going on right now, so not sure when I could get to it. In the mean time, you can access the sequences more easily in the sequence viewer, right click on the desired row / cell and copy-paste as tsv. Admittedly not ideal, but at least faster than having to go into the file elsewhere:
Thank you for the workaround. These specific primers have a non-hybridizing region (tail) and a hybridizing region (the rest). When I do what you suggested, only the part of the primers that hybridize are registered in the "Properties > Primers" section you show in the image (the same for "Sequence Map" section). However, the tail (non-hybridizing) sequence is dropped. I confirmed this with the real sequence of the primers from my local file in Snapgene.
Therefore, I think this workaround only works with primers with no 5' non-hybridizing sequences. I still can import the whole primers as you suggested.