The goal of this tutorial is to provide an educational introduction into some of the features that are provided by BioJava.
At the moment this tutorial is still under development. Please check the BioJava Cookbook for a more comprehensive collection of examples about what is possible with BioJava and how to do things.
The tutorial is intended to work with the most recent version of BioJava, although most examples will work with BioJava 3.0 and higher.
Book 1: The Core Module, basic working with sequences.
Book 2: The Alignment Module, pairwise and multiple alignments of protein sequences.
Book 3: The Structure Modules, everything related to working with 3D structures.
Book 4: The Genomics Module, working with genomic data.
Book 5: The Protein-Disorder Module, predicting protein-disorder.
Book 6: The ModFinder Module, identifying potein modifications in 3D structures
The content of this tutorial is available under the CC-BY license.
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.