BioJava

BioJava is an open-source software project dedicated to provide Java tools to process biological data. BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines. BioJava supports a huge range of data, starting from DNA and protein sequences to the level of 3D protein structures. The BioJava libraries are useful for automating many daily and mundane bioinformatics tasks such as to parsing a Protein Data Bank (PDB) file, interacting with Jmol and many more. This application programming interface (API) provides various file parsers, data models and algorithms to facilitate working with the standard data formats and enables rapid application development and analysis. These libraries have also been used in developing various extended analysis tools! for example:

The BioJava project grew out of work by Thomas Down and Matthew Pocock to create an API to simplify development of Java-based Bioinformatics tools. BioJava is an active open source project that has been developed over more than 12 years and by more than 60 developers. BioJava is one of a number of Bio* projects designed to reduce code duplication. Examples of such projects that fall under Bio* apart from BioJava are BioPython,BioPerl,BioRuby, EMBOSS etc.

Version 3.0.5 was a major update to the prior versions. It contained several independent modules. The old project has been moved to a separate project called BioJava-legacy project.

BioJava provides software modules for many of the typical tasks of bioinformatics programming. These include: