How do I specify consentrations of the different oligos in compiled NUPACK code for mfe and pairs excutables. I dont see it in the commands. I am using NUPACK 3.0.2.
Do I do complexes and then tweak the output file and run through Concentrations?
Would I even need to specify concentrations? If in the A / B puzzles 1st State for example TB-B at 100nM is supposed to bind but TB-A at 5nm is not. I would still just plug in the executable mfe -multi and use TB-B’s oligo only correct? Same for pairs if that is true.