Table 2 Energy functions for dangling bases
Function | Description |
|---|---|
dl _energy | A single base left of a closed substructure can dangle onto this stack and thus might further stabilize it. |
dr _energy | Symmetric case to dl _energy. |
ext _mismatch _energy | Two bases left and right of a stack, which do not form a basepair (they mismatch), can dangle from both sides to the stack. |
dli _energy | A multiloop is closed by one stack. A single base at the inside of the multiloop and directly next to the closing stack might dangle from left onto this stack. The energy values are the same as dr _energy, but for a reversed subsequence. |
dlr _energy | Symmetric case to dli _energy. |
ml _mismatch _energy | Two bases on both inner sides of a multiloop closing stack may dangle from inside onto this stack, but do not form a basepair (mismatch). |