COINCIDENCE · COMPATIBLE SUBSET · RNA FOLDING

From a helix subset
to dot-bracket

Every selected helix contributes paired positions: left bases become “(”, right bases become “)”, and unpaired bases remain “.”

PRIMARY STRUCTURE

RNA sequence

0 nt

SECONDARY STRUCTURE

Sequence and dot-bracket

———
RNA—
DBN—
Structural proxy score—lower is preferred; INN-HB deferred

SUBSET → PAIRS → SYMBOLS

How the transformation works

  1. 1Select mutually compatible helices.
  2. 2Expand (start, end, length) into (start+k, end−k).
  3. 3Write “(” on the left, “)” on the right, and keep other positions as dots.
selected = [(6,15,3)]
pairs    = [(6,15),(7,14),(8,13)]

.....(((....)))...

SELECTED PHENOTYPE

Helices used in this structure

REPRESENTATION

Selection inside a permutation

SARNA decodes a full priority permutation. Partition COIN makes selected | unselected explicit.

NEXT STEP

Reproduce, then extend

Next: exact paper helix generation, INN-HB tables, reference/Numba equivalence, then fair SARNA–GA–COIN experiments.