varVAMP - Set Primer Sequence Constraints

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I am using the varVAMP tool to design a pan primer set for enteroviruses, similar to this training project. However, I already own a hydrolysis probe and reverse primer that align across enteroviruses. I would like to input these sequences as required sequences for the forward primer design. At minimum, I would like to constrain the design to use the hydrolysis probe sequence, as this is a more expensive reagent to replace.

Is there a possible way to do this with the varVAMP tool?

Thanks for any help you may provide,
Dalton

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Wecome @Dalton_Nelson

Let’s get some advice from one of the tutorial authors. Hi @wm75 would you be able to advise or recommend one of the other authors? Thanks!

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@Dalton_Nelson thanks for trying out varVAMP. Unfortunately, the functionality you’d like to see is not yet implemented in the tool, but has already been discussed as a future improvement.
Since this sounds like a reasonable request, I will create an issue against the tool’s development repo, but someone needs to find the time to implement the feature.

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See Let users provide partial schemes to fill with varvamp · Issue #45 · jonas-fuchs/varVAMP · GitHub

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Thanks, @wm75 - happy to see nearly the exact tool I need actually exist! And thank you for promoting the implementation. I will try to move forward using the varVAMP generated consensus sequence and other tools (perhaps, IDT’s primer design tool) to try to overcome this current limitation.

Does the tool currently screen for dimerization when generating primer & probe sets? Perhaps, if the complexity is within bounds, I could consider helping the implementation in some of my future downtime.

Thanks for everything!

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Yes, it checks for dimers here:

and contributions are welcome of course :slight_smile: