BioJava: an open-source framework for bioinformatics in 2012

Andreas Prlic, Andrew Yates, Spencer E. Bliven, Peter W. Rose, Julius Jacobsen, Peter V. Troshin, Mark Chapman, Jianjiong Gao, Chuan Hock Koh, Sylvain Foisy, Richard Holland, Gediminas Rimsa, Michael L. Heuer, H. Brandstaetter-Mueller, Philip E. Bourne, Scooter Willis

    Research output: Contribution to journalArticlepeer-review

    138 Citations (Scopus)


    Motivation: 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.

    Original languageEnglish
    Pages (from-to)2693-2695
    Number of pages3
    Issue number20
    Publication statusPublished - 2012


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