BioJava: an open-source framework for bioinformatics in 2012.

TitleBioJava: an open-source framework for bioinformatics in 2012.
Publication TypeJournal Article
Year of Publication2012
AuthorsPrlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh C H, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstätter-Müller H, Bourne PE, Willis S
Date Published2012 Oct 15
KeywordsAmino Acids, Computational Biology, Genomics, Protein Conformation, Protein Processing, Post-Translational, Proteins, Sequence Alignment, Sequence Analysis, Sequence Analysis, DNA, Sequence Analysis, Protein, Software

UNLABELLED: 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 ( BioJava requires Java 1.6 or higher. All inquiries should be directed to the BioJava mailing lists. Details are available at

PubMed URL
Alternate JournalBioinformatics
PubMed ID22877863