BioJava is an open source project dedicated to providing Java tools for processing biological data. BioJava is a set of library functions written in the Java programming language for manipulating sequences, protein structures, file parsers, CORBA interoperability, 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 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 applica