Biobase.Secondary.Structure

A secondary structure, with sequence, Vienna compatible canonical secondary structure, extended structure, and additional information.

This is the structure that will be returned by prediction algorithms in the future.

TODO we will need ex- and import functions to a number of standard formats. There is an open feature request to export to something that resembles FASTA with additional information.

Documentation

data SecondaryStructure

A sequence, complete with secondary structure. While this structure is rather RNA-centric, there is nothing that prohibits us from using this for DNA.

TODO Generics, Cereal, Binary, Aeson instances

Constructors

SS

Fields

• _ssSeq :: !Text

  sequence; we use Text whenever possible

• _ssVienna :: !D1Secondary

  canonical Vienna secondary structure

• _ssExt :: !D2Secondary

  extended secondary structure

• _ssViennaE :: Maybe ()

  TODO will be the energy, measured or predicted

• _ssAux :: Map Text Text

  any auxiliary info in key/value format

Instances

Eq SecondaryStructure

Methods

(==) :: SecondaryStructure -> SecondaryStructure -> Bool

(/=) :: SecondaryStructure -> SecondaryStructure -> Bool

Read SecondaryStructure

Methods

readsPrec :: Int -> ReadS SecondaryStructure

readList :: ReadS [SecondaryStructure]

readPrec :: ReadPrec SecondaryStructure

readListPrec :: ReadPrec [SecondaryStructure]

Show SecondaryStructure

Methods

showsPrec :: Int -> SecondaryStructure -> ShowS

show :: SecondaryStructure -> String

showList :: [SecondaryStructure] -> ShowS