Package org.biopax.paxtools.model.level3

Interface FragmentFeature

All Superinterfaces:
BioPAXElement, Cloneable, EntityFeature, Level3Element, Observable, Serializable, UtilityClass
All Known Implementing Classes:
FragmentFeatureImpl
public interface FragmentFeature extends EntityFeature
Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or degradation event. Usage: Fragment Feature can be used to cover multiple types of modfications to the sequence of the physical entity:
  • A protein with a single cleavage site that converts the protein into two fragments (e.g. pro-insulin converted to insulin and C-peptide). TODO: CV term for sequence fragment? PSI-MI CV term for cleavage site?
  • A protein with two cleavage sites that removes an internal sequence e.g. an intein i.e. ABC -> A
  • Cleavage of a circular sequence e.g. a plasmid.
In the case of removal ( e.g. intron) the fragment that is *removed* is specified in the feature location property. In the case of a "cut" (e.g. restriction enzyme cut site) the location of the cut is specified instead. Examples: Insulin Hormone