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adding an initial chapter for protein-disorder
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‎README.md‎

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A brief introduction into [BioJava 3](https://github.com/biojava/biojava).
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==
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==
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The goal of this tutorial is to provide an educational introduction into some of the features that are provided by BioJava.
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The goal of this tutorial is to provide an educational introduction into some of the features that are provided by BioJava.
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At the moment this tutorial is still under development. Please check the [BioJava Cookbook](http://biojava.org/wiki/BioJava:CookBook3.0) for a more comprehensive collection of many examples of what is possible with BioJava and how to do things.
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Book 4: [The Genomics Module](genomics/README.md), working with genomic data
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Book 5: [The Protein-Disorder Module](protein-disorder/README.md), predicting protein-disorder.
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## License
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‎protein-disorder/README.md‎

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The Protein-Disorder Module of BioJava
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=====================================================
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A tutorial for the protein-disorder module of [BioJava](http://www.biojava.org)
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## About
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<table>
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<tr>
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<td>
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</td>
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<td>
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The <i>protein-disorder module</i> of BioJava provide an API that allows to
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<ul>
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<li>predict protein-disorder using the JRONN algorithm</li>
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</ul>
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</td>
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</tr>
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</table>
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## How can I predict disordered regions on a protein sequence?
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-----------------------------------------------------------
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BioJava provide a module *biojava-protein-disorder* for prediction
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disordered regions from a protein sequence. Biojava-protein-disorder
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module for now contains one method for the prediction of disordered
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regions. This method is based on the Java implementation of
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[RONN](http://www.strubi.ox.ac.uk/RONN) predictor.
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This code has been originally developed for use with
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[JABAWS](http://www.compbio.dundee.ac.uk/jabaws). We call this code
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*JRONN*. *JRONN* is based on the C implementation of RONN algorithm and
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uses the same model data, therefore gives the same predictions. JRONN
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based on RONN version 3.1 which is still current in time of writing
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(August 2011). Main motivation behind JRONN development was providing an
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implementation of RONN more suitable to use by the automated analysis
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pipelines and web services. Robert Esnouf has kindly allowed us to
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explore the RONN code and share the results with the community.
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Original version of RONN is described in [Yang,Z.R., Thomson,R.,
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McMeil,P. and Esnouf,R.M. (2005) RONN: the bio-basis function neural
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network technique applied to the detection of natively disordered
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regions in proteins. Bioinformatics 21:
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3369-3376](http://bioinformatics.oxfordjournals.org/content/21/16/3369.full)
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Examples of use are provided below. For more information please refer to
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JronnExample testcases.
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Finally instead of an API calls you can use a [ command line
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utility](/wikis/BioJava:CookBook3:ProteinDisorderCLI "wikilink"), which is
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likely to give you a better performance as it uses multiple threads to
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perform calculations.
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Example 1: Calculate the probability of disorder for every residue in the sequence
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----------------------------------------------------------------------------------
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```java
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FastaSequence fsequence = new FastaSequence("name",
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"LLRGRHLMNGTMIMRPWNFLNDHHFPKFFPHLIEQQAIWLADWWRKKHC" +
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"RPLPTRAPTMDQWDHFALIQKHWTANLWFLTFPFNDKWGWIWFLKDWTPGSADQAQRACTWFFCHGHDTN");
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float[] rawProbabilityScores = Jronn.getDisorderScores(fsequence);
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```
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Example 2: Calculate the probability of disorder for every residue in the sequence for all proteins from the FASTA input file
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-----------------------------------------------------------------------------------------------------------------------------
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```java
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final List<FastaSequence> sequences = SequenceUtil.readFasta(new FileInputStream("src/test/resources/fasta.in"));
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Map<FastaSequence, float[]> rawProbabilityScores = Jronn.getDisorderScores(sequences); ```
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Example 3: Get the disordered regions of the protein for a single protein sequence
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----------------------------------------------------------------------------------
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```java
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FastaSequence fsequence = new FastaSequence("Prot1", "LLRGRHLMNGTMIMRPWNFLNDHHFPKFFPHLIEQQAIWLADWWRKKHC" +
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               "RPLPTRAPTMDQWDHFALIQKHWTANLWFLTFPFNDKWGWIWFLKDWTPGSADQAQRACTWFFCHGHDTN" +
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               "CQIIFEGRNAPERADPMWTGGLNKHIIARGHFFQSNKFHFLERKFCEMAEIERPNFTCRTLDCQKFPWDDP");
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Range[] ranges = Jronn.getDisorder(fsequence);
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```
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Example 4: Calculate the disordered regions for the proteins from FASTA file
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----------------------------------------------------------------------------
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```java
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final List<FastaSequence> sequences = SequenceUtil.readFasta(new FileInputStream("src/test/resources/fasta.in"));
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Map<FastaSequence, Range[]> ranges = Jronn.getDisorder(sequences);
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```
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### Author:
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[Andreas Prli&#263;](https://github.com/andreasprlic)
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## Please cite
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**BioJava: an open-source framework for bioinformatics in 2012**<br/>
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*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* <br/>
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[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) <br/>
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[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863)
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## License
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The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license.
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[view license](../license.md)
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<!--automatically generated footer-->
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---
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Navigation:
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[Home](../README.md)
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| Book 3: The Protein Structure modules
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Prev: [Book 4: The Genomics Module](../genomics/README.md)

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