Biobase.Secondary.Isostericity

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

Documentation

class IsostericityLookup a where

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.

Minimal complete definition

getClasses, inClass

Methods

getClasses :: a -> [String]

To which classes does a basepair+type belong

inClass :: String -> [a]

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

Methods

getClasses :: ExtPair -> [String]

inClass :: String -> [ExtPair]

IsostericityLookup Pair

Normal basepairs are assumed to have cWW basepairing.

TODO inClass missing

Methods

getClasses :: Pair -> [String]

inClass :: String -> [Pair]

default data

defaultIsostericityMap :: Map ExtPair [String]

The default isostericity mapping.

mkIsostericityMap :: [[[String]]] -> Map ExtPair [String]

Mapping of (pair,pairtype) to isostericity class.

mkIsostericityList :: [[[String]]] -> [(ExtPair, [String])]

Process CSV list-of-lists to get the isostericity data.

parsedCSV :: [[[[Char]]]]

Simple parsing of raw CSV data.

Raw embeddings

detailedCSV :: ByteString

Raw CSV data, embedded into the library.