BioJava: an open-source framework for bioinformatics in 2012

Abstract

BioJava is an open-source project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality.

Results: BioJava now consists of several independent modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model.

Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.6 or higher. All inquiries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists.

Fig. 1.

An example application using the ModFinder module and the protein structure module. Protein modifications are mapped onto the sequence and structure of ferredoxin I (PDB ID 1GAO; Chen et al., 2002). Two possible iron–sulfur clusters are shown on the protein sequence (3Fe–4S (F3S): orange triangles/lines; 4Fe–4S (SF4): purple diamonds/lines). The 4Fe–4S cluster is displayed in the Jmol structure window above the sequence display