Set plasmid origin

[cesaravila79]

Hi @manulera,
I am new to OpenCloning, and still trying its different features. I have successfully used it for sub cloning and site directed mutagenesis. Nevertheless, there is still one small feature that I would like to see in the workflow, and it is the possibility to align a new plasmid with its parent. Let me expand on that. I read a plasmid from the database, and performed a PCR with custom primers to introduce a point mutation, and later on I circularized it. The thing is that the resulting plasmid has a new origin (the base that you arbitrarily take as 1 in a circular plasmid, not the origin of replication) that I think is aligned with the primer. I would like to "renumber" the bases to match those in the original plasmid.
Best regards,
Cesar

[manulera]

Hi @cesaravila79 thanks for the feedback, some things:

If you just want to "compare" both plasmids, I am planning a feature to select sequences from the interface and produce a Multiple Sequence Alignment, would that be enough?.

In the mean time, you can do a bit of a "hack". You can download one of the two plasmids as a genbank file (clicking on the down-pointing arrow on the top-right corner of the interface). Then, align it with the other plasmid as if it was sequencing data (see the video).

output.mp4

If this is not enough, I could eventually implement a rotation operation (like the reverse-complement option)

[cesaravila79]

That's right, a way to rotate it in addition to flip it would be great for those of us that need to have them all oriented in the same way 😅. In addition to the manual rotation/flip operations I would include an "automatic " rearrangement to maximize the alignment score with a reference.

[benweinberg89]

shifted() accomplishes this in pydna. perhaps can be applied here? i usually search for first 20-50bp of where the new plasmid should start, find the index, and then pipe into shifted.

[manulera]

Thanks @benweinberg89 this can be indeed done using shifted, I just have a lot going on right now so I have not prioritised it. By the way @cesaravila79 if you want to prioritise the development of this feature, you can always pay for a custom development. If you are interested on this, please reach out