Strategy for Exclusion labs (Turnoff labs)
Give 3+ if there is a 2 base pair stack forming close in front of the MS2 when it is forming. That stack in front of the MS2 is what I call MS2 gate.
Give 2+ if there is a 3 base pair stack forming and decrease score for length hereafter.
Give +1 if that MS2 gate is spaced by a energy weak 1-1 loop, a bulge right in front of the MS2 or a small internal loop or bulge (max 4 bases away) in between MS2 and the MS2 gate, when the MS2 is forming. Preferable with most of the single bases before the MS2. This spacer between MS2 and MS2 gate strategy, goes for MicroRNA labs too.
Strategy for Same state labs (Turn on labs)
If there are any MS2 gate forming in an average of 0-3 bases away from the MS2 (max 4 base distance on either side) hairpin, when MS2 is forming. Penalize harshly and exponentially per base pair count in the MS2 gate.
Strategy for MicroRNA labs
Give bonus to MS2 Gates for Turn on labs (sensor 208a), that are 5 bp long. Decrease bonus for more or less.
Give bonus for MS2 Gate for Turnoff labs, that are 6-9 bp long. Decrease bonus for more or less.
Background articles
The MS2 gates are visualized in the post below:
https://getsatisfaction.com/eternagam…