BioInf.Nussinov78

Strict, scalar nussinov78 algorithm.

Documentation

nussinov78 :: MkPrimary a => a -> [Backtrace]

Simple RNA folding with basepair maximization.

nussinov78Fill :: Primary -> ST s (Arr0 DIM2 Int)

The actual Nussinov78 folding algorithm.

fillTable :: PrimMonad m => MArr0 (PrimState m) DIM2 Int -> (DIM2 -> m Int) -> m ()

Fill the single table with values in an orderly fashion. The order in which we fill depends on the algorithm.

base' :: Primary -> DIM2 -> Scalar Nuc

Request the single character enclosed by (i,i+1), with i+1==j

empty :: DIM2 -> Scalar Bool

True, if the subword at ij is empty.

nil :: Bool -> Int

The base case of our recursion.

left :: Nuc -> Int -> Int

A single nucleotide to the left. Note that x is monadic. In nussinov we are in the ST monad, here we just know that we are in a monad.

right :: Int -> Nuc -> Int

A single nucleotide to the right.

pair :: Nuc -> Int -> Nuc -> Int

Pair function

split :: Int -> Int -> Int

Combine the partition of x next-to y.

basepair :: MkViennaPair (t, t1) => t -> t1 -> Bool

Determine if two characters form a legal basepair.

h :: (Monad m, Ord a) => Stream m a -> m a

the grammar makes sure that we at least have nil in the stream

backtrace secondary structures

type Backtrace = (Int, String)

nussinov78BT :: Primary -> Arr0 DIM2 Int -> [Backtrace]