BiobaseTrainingData- RNA folding training data





data TrainingData Source

One training data element. We can store sequence and known structure (primary, secondary) as well as a predicted structure (stored, if not.null). The weight is how strongly this element should influence a training system. extendedKnowledge is True, if the data element comes from a source which knows about extended secondary structures, like the PDB. Otherwise it is False.

NOTE During training, one should not penalize non-canonical predictions in interior loops and multibranch loops, unless they hinder formation of true pairs.

TODO at some point we will move toward pseudoknots and other fun

Instance creation

class MkTrainingData a whereSource

Create TrainingData from various sources.


MkTrainingData RNAstrand

Import from RNAstrand data. Each annotated pair is assumed to be of type cWW.

MkTrainingData LinFR3D

Import from linearized FR3D data