I woke up two days ago with a crazy idea for a strategy. Here it comes:
The neckarea is regulary a pain in the neck. I would like a strategy, that re-use necks that is known to work and be highly succesfull. Sort of a catalog of necks, for that length of neck, the design has.
Importing necks have worked better, than import of other elements. Aldo took the neck from nupack bot design 1 (branches) and since it have been recirculated in other designs with great succes. It appears in a 100% design in both branches and asymmetry lab. There are high rate of repetitive patterns in necks, that equals fewer legal placements of nucleotides than elsewhere in the design. That is why this might work.
Changing only the neck in a design, often gives an improvement of the score on 3%, sometimes up to 5%, even if both necks are working and without mispairings. (Have a post on this comming)
Strategy for picking of necks. Pick working necks with no mispairings, no matter the score of the design they appear in. That will pick up the working necks from bots too – which is good – as they generally are good at making necks.
But rank the necks based on the average of the score of the designs they appear in, when working. A neck that appears with succes in many highscoring designs, will achieve a high score it self. Over time necks which are good will show themselves.