Biobase.Secondary.Isostericity
Contents
Description
Provides detailed information on isostericity of RNA basepairs. All data is extracted from csv files which were created from supplemental files in:
Frequency and isostericity of RNA base pairs Jesse Stombaugh, Craig L. Zirbel, Eric Westhof, and Neocles B. Leontis Nucl. Acids Res. (2009) doi:10.1093nargkp011
- class IsostericityLookup a where
- getClasses :: a -> [String]
- inClass :: String -> [a]
- mkIsostericityList :: [[[String]]] -> [(ExtPair, [String])]
- detailedCSV :: ByteString
Documentation
class IsostericityLookup a whereSource
Methods to determine the isostericity classes for a given basepair type, or alternatively which basepair types are in a certain isostericity class.
TODO This requires a major cleanup: right now we are handling Strings as
class descriptors, but we should really be newtype-wrapping or create enum
data constructors.
Methods
getClasses :: a -> [String]Source
To which classes does a basepair+type belong
inClass :: String -> [a]Source
What basepairs+type are in a particular class
Instances
| IsostericityLookup ExtPair | For extended basepairs, we take the default mapping and go from there. TODO inClass missing |
| IsostericityLookup Pair | Normal basepairs are assumed to have cWW basepairing. TODO inClass missing |
default data
mkIsostericityList :: [[[String]]] -> [(ExtPair, [String])]Source
The default isostericity mapping.
Mapping of (pair,pairtype) to isostericity class.
Process CSV list-of-lists to get the isostericity data.
Raw embeddings
detailedCSV :: ByteStringSource
Raw CSV data, embedded into the library.