Package org.biojava.nbio.ronn
BioJava provide a module biojava-protein-disorder for prediction disordered regions from a protein sequence. Biojava-protein-disorder module for now contains one method for the prediction of disordered regions. This method is based on the Java implementation of RONN predictor.
This code has been originally developed for use with JABAWS. We call this code JRONN. JRONN is based on the C implementation of RONN algorithm and uses the same model data, therefore gives the same predictions. JRONN based on RONN version 3.1 which is still current in time of writing (August 2011). Main motivation behind JRONN development was providing an implementation of RONN more suitable to use by the automated analysis pipelines and web services. Robert Esnouf has kindly allowed us to explore the RONN code and share the results with the community.
Original version of RONN is described in Yang,Z.R., Thomson,R., McMeil,P. and Esnouf,R.M. (2005) RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 21: 3369-3376
Examples of use are provided below. For more information please refer to JronnExample testcases.
- Since:
- 3.0.2
- Version:
- 1.0 January 2010
- Author:
- Peter Troshin
-
Class Summary Class Description Jronn This class gives public API to RONN functions.Jronn.Range Holder for the ranges, contain pointers to starting and ending position on the sequence which comprises a disordered region.ModelLoader Class that loads data from the model files intoModelLoader.ModelobjectsModelLoader.Model Represent a RONN modelModelLoader.Threshold Represents a ThresholdNullOutputStream The stream that void its inputORonn Fully re-factored and enhanced version of RONN.ORonnModel Fully re-factored version of RONN model.RonnConstraint A collection of various constrain values used by RONNTimer A simple timer, calculates the time interval between two events. -
Enum Summary Enum Description RonnConstraint.Threshold