BiobaseXNA-0.11.0.0: Efficient RNA/DNA/Protein Primary/Secondary Structure

Safe HaskellNone
LanguageHaskell2010

Biobase.Secondary.Pseudoknots

Description

Methods to transform a secondary structure containing pseudoknots into a structure which is pseudoknot-free.

TODO Until a better name is found, this module is home to functions for "de-pseudoknotting" structures.

TODO Check if there are corner-cases remaining when considering 2-diagrams.

Synopsis

Documentation

class RemovePseudoKnots a where Source #

Try to removed pseudoknots from the "pairlist". This works by counting for each pair, how many pairs are incompatible with it. Then those with most incompatibilities are successively removed. This function might well remove more than necessary!

Methods

removeByCounting :: a -> a Source #

Instances
RemovePseudoKnots [ExtPairIdx] Source # 
Instance details

Defined in Biobase.Secondary.Pseudoknots

RemovePseudoKnots [PairIdx] Source # 
Instance details

Defined in Biobase.Secondary.Pseudoknots

RemovePseudoKnots (Vector ExtPairIdx) Source #

Remove pseudoknotted pairs from extended RNA secondary structures.

Instance details

Defined in Biobase.Secondary.Pseudoknots

RemovePseudoKnots (Vector PairIdx) Source #

Remove pseudoknotted pairs from RNA secondary structures.

Instance details

Defined in Biobase.Secondary.Pseudoknots