Protein Structure Modules
provide an API that allow to
- Maintain local installations of PDB
- Load structures and manipulate them
- Perform standard analysis such as sequence and structure alignments
- Visualize structures
BioJava is open source
It's hosted, developed, and maintained on GitHub.
- Current release: 5.0.0
- Ipsum
- Dolor
Protein Structure Modules
Biological Sequences
BioJava allows to
- Perform basic operations on biological sequences
- Read and Write popular sequence file formats
- Translate DNA sequences into protein 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.
Mailing list
Questions, comments, and communications regarding BioJava can be made either on github or on the BioJava mailing list:
- biojava-l general discussion list
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Tutorial
The tutorial offers an introduction into some of the features that are provided by BioJava.
tutorial -
Cookbook
The Cookbook provides simple coding recipes that follow a "How do I ..." approach.
Cookbook -
Javadoc API
The Javadocs for the current BioJava release
Javadoc API -
Current release: 5.0.0
BioJava is available from Maven Central
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Wiki
All pages from the legacy wiki site have been migrated to markdown pages
View wiki -
Legacy Javadoc API
The Javadocs for legacy 1.x BioJava.
View 1.9.1 API
Learn More
Here a couple of pointers for how to get started