generating a dot plot for a switch state with apatemer bonus

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Is anyone familiar with how one could generate dot-plot data for a switch state with an aptamer bonus? I know how to use the ViennaRNA software library to generate a dot-plot in the standard mode, which is very fast for designs of length 85.  But is is possible to efficiently compute a dot-plot (not just an MFE) to represent applying an energy bonus for an aptamer forming or not?
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jandersonlee

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Posted 1 year ago

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Brourd

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I'm personally not too sure of how easy it would be to modify the ViennaRNA libraries, but I imagine that if you were to encode a free energy bonus/special exception for an aptamer loop with a specific loop sequence/structure, then your resulting MFE, partition function, and pairing probabilities should reflect the population of structures that contain your special exception.
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jandersonlee

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When I constrain the pair bonding to designs with a fixed subshape (as an aptamer), it seems to only credit those suboptimal foldings that have those bonds. What I then do is multiply the constrained bonding probabilities by a scaling factor to mimic the aptamer bonus, add them to the unconstrained probabilities, then rescale the overall probabilities such that the totals for each column (base) add up to no more than 1.0. This seems to give a dot-plot image that boosts the aptamer containing shapes while maintaining a shadow version of the non-aptamer shapes that are absent from the original constrained dot-plot.
(Edited)