BiobaseXNA-0.5.6.0: Efficient RNA/DNA representations

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 whereSource

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 -> aSource

Instances

RemovePseudoKnots [ExtPairIdx] 
RemovePseudoKnots [PairIdx] 
RemovePseudoKnots (Vector ExtPairIdx)

Remove pseudoknotted pairs from extended RNA secondary structures.

RemovePseudoKnots (Vector PairIdx)

Remove pseudoknotted pairs from RNA secondary structures.