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‎README.md‎

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<img src="logo.png" height="30"/> Tutorial
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===
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A brief introduction into [BioJava](https://github.com/biojava/biojava).
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A brief introduction into [BioJava](https://www.biojava.org).
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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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## Index
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Quick [Installation](installation.md)
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[Quick Installation](installation.md)
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Book 1: [The Core Module](core/README.md), basic working with sequences.
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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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The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](license.md).
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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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**BioJava 5: A community driven open-source bioinformatics library**<br/>
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*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/>
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[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
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[![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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<!--automatically generated footer-->

‎alignment/README.md‎

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Chapter 6 - BLAST - why you don't need BioJava for parsing BLAST
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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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The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](../license.md).
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## Please cite
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[view license](../license.md)
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**BioJava 5: A community driven open-source bioinformatics library**<br/>
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*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/>
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[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
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[![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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‎core/README.md‎

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Chapter 4 - [Translating](translating.md) DNA and protein sequences.
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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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The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](license.md).
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## Please Cite
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[view license](../license.md)
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**BioJava 5: A community driven open-source bioinformatics library**<br/>
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*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/>
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[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
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[![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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‎genomics/README.md‎

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Chapter 6 - Reading genomic DNA sequences using UCSC's [.2bit file format](twobit.md)
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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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The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](license.md).
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## Please Cite
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[view license](../license.md)
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**BioJava 5: A community driven open-source bioinformatics library**<br/>
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*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/>
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[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
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[![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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‎modfinder/README.md‎

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Chapter 4 - [How to define a new protein modification](add-protein-modification.md)
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## Please cite
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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, available [here](license.md).
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## Please Cite
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**BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank**<br/>
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*Jianjiong Gao; Andreas Prlic; Chunxiao Bi; Wolfgang F. Bluhm; Dimitris Dimitropoulos; Dong Xu; Philip E. Bourne; Peter W. Rose* <br/>
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[Bioinformatics. 2017 Feb 17.](https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx101) <br/>
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[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbtx101-blue.svg?style=flat)](https://doi.org/10.1093/bioinformatics/btx101) [![pubmed](http://img.shields.io/badge/pubmed-28334105-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/28334105)
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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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**BioJava 5: A community driven open-source bioinformatics library**<br/>
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*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/>
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[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
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[![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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‎protein-disorder/README.md‎

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```
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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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The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](license.md).
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## Please Cite
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[view license](../license.md)
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**BioJava 5: A community driven open-source bioinformatics library**<br/>
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*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/>
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[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
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[![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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‎structure/README.md‎

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Chapter 18 - [Lists](lists.md) of PDB IDs and PDB [Status Information](lists.md)
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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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The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](license.md).
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## Please Cite
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[view license](../license.md)
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**BioJava 5: A community driven open-source bioinformatics library**<br/>
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*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/>
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[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
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[![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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