BioInf.RNAwolf.Stem

Collapses an extended stem into a normal stem, or allows going back from a

fNstem :: BaseF (EStem -> Features (Vector (ExtPairIdx, Double)))

A normal stem is created by taking the minimum over all possible basepairs of the extended stem.

btNstem :: Params -> Primary -> NStem -> EStem -> ExtBT -> NBT

Backtrack from a normal stem back into the extended stem.

Stacking with extended basepair information

fStem :: BaseF (EStem -> ExtFeatures (Vector (ExtPairIdx, Double)))

A stem is extended by another pair. The score contribution is dependent on the previous pair. Note that for score lookup purposes, the inner pair is switched.

btStem :: Params -> Primary -> EStem -> ExtBT -> ExtBT

Stem backtracking.