>Background: RNA primary and secondary structure. Working on the RNA design problem (Inverse RNA folding.) [Ah, the memories…]
Divide into sequence space and structure space. Structure space is smaller than sequence space. (Many to one relationship.)
Biology application: how does sequence mutation change the structure space?
Neighbourhood Ball : Sequences that are closely related, but fold differently. As you get closer to the edge of the ball, you find… [something?]
- Sample n sequences with unique mapping strucure
- for each sample: search neutral sequence within inner layers, redundancy hit?
- Compute redundancy rate p.
- Redundancy rate distribution over Hamming layers. P will approach 1. (all structure are redundant.)
The question is at what point do you saturate? Where do you find this boundary? Somewhere around 50% of sequence space. [I think??]
- An efficient estimation boundary – confirmed the existence of the neigborhood ball
- ball radius is much smaller than the seqeunce length.
Where is this useful?
- Reduce computational effort for RNA design
- naturally occurring RNA molecules, faster reduncdancy growth rate suggests mutational robustness.