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The Protein-Disorder Module of BioJava

A tutorial for the protein-disorder module of BioJava

About

    </td>
    <td>
        The <i>protein-disorder module</i> of BioJava provide an API that allows to
        <ul>
            <li>predict protein-disorder using the JRONN algorithm</li>
        </ul>


    </td>
</tr>

How can I predict disordered regions on a protein sequence?

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.

Finally instead of an API calls you can use a command line utility, which is likely to give you a better performance as it uses multiple threads to perform calculations.

Example 1: Calculate the probability of disorder for every residue in the sequence

FastaSequence fsequence = new FastaSequence("name",
  "LLRGRHLMNGTMIMRPWNFLNDHHFPKFFPHLIEQQAIWLADWWRKKHC" +
  "RPLPTRAPTMDQWDHFALIQKHWTANLWFLTFPFNDKWGWIWFLKDWTPGSADQAQRACTWFFCHGHDTN");

float[] rawProbabilityScores = Jronn.getDisorderScores(fsequence);

Example 2: Calculate the probability of disorder for every residue in the sequence for all proteins from the FASTA input file

final List<FastaSequence> sequences = SequenceUtil.readFasta(new FileInputStream("src/test/resources/fasta.in"));
Map<FastaSequence, float[]> rawProbabilityScores = Jronn.getDisorderScores(sequences);

Example 3: Get the disordered regions of the protein for a single protein sequence

FastaSequence fsequence = new FastaSequence("Prot1", "LLRGRHLMNGTMIMRPWNFLNDHHFPKFFPHLIEQQAIWLADWWRKKHC" +
               "RPLPTRAPTMDQWDHFALIQKHWTANLWFLTFPFNDKWGWIWFLKDWTPGSADQAQRACTWFFCHGHDTN" +
               "CQIIFEGRNAPERADPMWTGGLNKHIIARGHFFQSNKFHFLERKFCEMAEIERPNFTCRTLDCQKFPWDDP");

Range[] ranges = Jronn.getDisorder(fsequence);

Example 4: Calculate the disordered regions for the proteins from FASTA file

final List<FastaSequence> sequences = SequenceUtil.readFasta(new FileInputStream("src/test/resources/fasta.in"));
Map<FastaSequence, Range[]> ranges = Jronn.getDisorder(sequences);

Please cite

BioJava: an open-source framework for bioinformatics in 2012
Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis
Bioinformatics (2012) 28 (20): 2693-2695.
doi pubmed

License

The content of this tutorial is available under the CC-BY license.

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