Protein structures
BioJava provides an API to maintain local installations of the PDB, load and manipulate structures, perform standard analysis such as sequence and structure alignments and visualize them in 3D.
Open source
The project is hosted, developed, and maintained on GitHub.
GitHub project
Biological sequences
BioJava supports reading and writing popular sequence file formats, translating DNA sequences into proteins and other common bioinformatics routines.
Please cite
BioJava 5: A community driven open-source bioinformatics library
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
PLOS Computational Biology (2019) 15 (2):e1006791.
Get in touch
Questions, comments, and communications regarding BioJava can be done either on GitHub or through the BioJava mailing list. Subscribe to stay up to date!
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Tutorial
The tutorial offers an introduction into some of the features provided by BioJava.
Tutorial -
CookBook
The Cookbook provides simple coding recipes to common bioinformatics problems using BioJava.
Cookbook -
Javadoc API
The Javadocs for the current BioJava 6.1.0 release.
Javadoc API -
Release 6.1.0
BioJava is available from Maven Central.
Maven Central -
Wiki
All pages from the legacy wiki site have been migrated to markdown pages
View wiki -
Legacy Javadoc API
The Javadocs for BioJava legacy 1.x versions.
View 1.9.5 API
Learn More
Here a couple of pointers to get you started