RNAFold- RNA secondary structure prediction



Given a sequence and a structure, evaluate the energy.

TODO switch to 'SSTree [Energy]' type!



rnaEval :: ViennaTables -> String -> String -> IntSource

Sum up a complete (sub-) tree.

annotateWithEnergy :: ViennaTables -> Primary -> SSTree () -> SSTree [Int]Source

Evaluate the energy of a secondary structure tree with sequence. We abuse the normal folding functions with a dummy table full of (one :: Energy). This is probably slower than another method but quickly written.

TODO this is basically crapfuck ;-) Should use the FoldFunctions directly instead of that strange table. Should not xxxOpt either.

explainTree :: Primary -> SSTree [Int] -> [String]Source

convert an annotated tree into strings that explain each score.

TODO this is a stupid name