A brief introduction into BioJava.
The goal of this tutorial is to provide an educational introduction into some of the features that are provided by BioJava. This tutorial is still under development, hence not yet comprehensive for the entire library. Please also check other sources of documentation.
The examples within the tutorial are intended to work with the most recent version of BioJava, although most examples will work with BioJava 3.0 and higher. Please do submit a new issue if you find any problems.
The tutorial is subdivided into several books, corresponding to the respective BioJava modules. Each book is further subdivided into several chapters that intend to describe the main functionality of the module in order of increasing complexity.
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, available here.
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.