So I had an idea for a way to analyze multi-oligo sublabs with Vienna 2. Since only one oligo supposed to be bound in each state what if I just modeled each state with the correct oligo present which is only one. Would that be valid? If so I could do an analysis and give predictions hopefully on the A/B with predefinded binding sites quickly.I am not sure I understand if I need to use NUPACKS concentrations program for the multi-oligo labs as well.
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