Biobase.Turner
Description
The Turner2004 data structure reflects the RNA (and DNA) energy
parameters known as the Turner 2004 data set.
In general, have a look here: http://rna.urmc.rochester.edu/NNDB/turner04/index.html where parameters are explained.
- data Turner2004 = Turner2004 {
- stack :: PrimArray (Pair, Pair) Double
- dangle3 :: PrimArray PN Double
- dangle5 :: PrimArray PN Double
- hairpinL :: PrimArray Int Double
- hairpinMM :: PrimArray PNN Double
- hairpinLookup :: Map ByteString Double
- hairpinGGG :: Double
- hairpinCslope :: Double
- hairpinCintercept :: Double
- hairpinC3 :: Double
- bulgeL :: PrimArray Int Double
- bulgeSingleC :: Double
- iloop1x1 :: PrimArray (Pair, Pair, (Nuc, Nuc)) Double
- iloop2x1 :: PrimArray (Pair, Pair, (Nuc, Nuc, Nuc)) Double
- iloop2x2 :: PrimArray (Pair, Pair, (Nuc, Nuc, Nuc, Nuc)) Double
- iloopMM :: PrimArray PNN Double
- iloop2x3MM :: PrimArray PNN Double
- iloop1xnMM :: PrimArray PNN Double
- iloopL :: PrimArray Int Double
- multiMM :: PrimArray PNN Double
- ninio :: Double
- maxNinio :: Double
- multiOffset :: Double
- multiNuc :: Double
- multiHelix :: Double
- multiAsym :: Double
- multiStrain :: Double
- extMM :: PrimArray PNN Double
- coaxial :: PrimArray (Pair, Pair) Double
- coaxStack :: PrimArray PNN Double
- tStackCoax :: PrimArray PNN Double
- largeLoop :: Double
- termAU :: Double
- intermolecularInit :: Double
- type PNN = (Pair, Nuc, Nuc)
- type PN = (Pair, Nuc)
Documentation
data Turner2004 Source
The parameters. Turner parameters are set by the Import module for nucleotides n,a,c,g,u. All values that are not read (or are .) will end up with a value > 100K.
- 1
- Yes, such instances are easily created, but I don't want to pull in another library and I don't want to create an Ix instance here.
TODO use Energy instead of Double
Constructors
Instances