Table 1 Secondary structure operators. Operators build terms by application to (sub-)terms. Operators can be interpreted in different ways with algebras, such as the Boltzmann-weighted energy algebra. In this case, terms evaluate to real numbers. Interpreting operators as mere symbols leads to symbolic terms that represent structures, (cf. also Figure 1)
operator | description |
|---|---|
SS(l) | single-stranded region l |
HL(a,l,b) | hairpin loop with single stranded region l, closed by basepair (a,b) |
SR(a,x,b) | stacking region, closed by basepair (a,b); x is a closed structure |
BL(a,l,x,b) | bulge left with single stranded region l, closed by basepair (a,b); x is a closed structure |
BR(a,x,l,b) | bulge right with single stranded region l, closed by basepair (a,b); x is a closed structure |
IL(a,l,x,l',b) | internal loop with single stranded regions l and l', closed by basepair (a,b); x is a closed structure |
ML(a,c,b) | multi-loop, closed by basepair (a,b) |
AD(x,c) | list of adjacent structures; x is a structure, c a (possibly empty) list of adjacent structures |
E | empty list of adjacent structures |