The BioJava - Genomics Module
=====================================================

A tutorial for the genomics module of [BioJava](http://www.biojava.org)

## About
<table>
    <tr>
        <td>
            <img src="img/genomics.png"/>
        </td>
        <td>
            The <i>genome</i> module of BioJava provides an API that allows to
            <ul>
                <li>Parse popular file formats used in genomcs</li>
                <li>Convert from one file format to another</li>
                <li>Translate DNA sequences into protein sequences</li>                
            </ul>
        </td>
    </tr>
</table>   

## Index

This tutorial is split into several chapters.

Chapter 1 - Quick [Installation](installation.md)

Chapter 2 - Reading [gene names information](genenames.md) from genenames.org

Chapter 3 - Reading [chromosomal positions](chromosomeposition.md) for genes. (UCSC's refFlat.txt.gz )

Chapter 4 - Reading [GTF and GFF files](gff.md)

Chapter 5 - Reading and writing a [Genebank](genebank.md) file

Chapter 5 - Reading [karyotype (cytoband)](karyotype.md) files

Chapter 6 - Reading genomic DNA sequences using UCSC's [.2bit file format](twobit.md)


## License

The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](../license.md).

## Please Cite

**BioJava 5: A community driven open-source bioinformatics library**<br/>
*Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte* <br/>
[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
[![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006791-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006791) [![pubmed](https://img.shields.io/badge/pubmed-30735498-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/30735498)



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