One continuing puzzle about the results from the Perl simulation of uptake sequence variation is the independence of equilibrium score and mutation rate. It's true that mutations both create and destroy uptake sequences, but I wouldn't expect the effects to consistently cancel each other out. Even though that's what happened in a very simple mathematical model I did years ago.
I suspect that the interactions between mutation and uptake sequence accumulation are more subtle than their independence would seem to suggest. So here are several questions that I think I can quickly answer with more runs:
1. Does changing the proportionality of µg and µf change the equilibrium? (I already know there's about a 2-fold equilibrium score difference between 100:1 and 100:100, but I want to test more proportions.)
2. Does changing fragment length but keeping the number of fragments recombined per cycle the same change the equilibrium?
3. Does changing the fragment length but keeping the amount of DNA recombined the same change the equilibrium?
4. When µf = µg, does changing the fragment length but keeping the number of fragments recombined per cycle the same have no effect? Maybe not, because long fragments are more likely to change other US?
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