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 journalArticle

    110 Citations (Scopus)

    Abstract

    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
    JournalBioinformatics
    Volume28
    Issue number20
    DOIs
    Publication statusPublished - 2012

    Cite this

    Prlic, A., Yates, A., Bliven, S. E., Rose, P. W., Jacobsen, J., Troshin, P. V., ... Willis, S. (2012). BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics, 28(20), 2693-2695. https://doi.org/10.1093/bioinformatics/bts494
    Prlic, Andreas ; Yates, Andrew ; Bliven, Spencer E. ; Rose, Peter W. ; Jacobsen, Julius ; Troshin, Peter V. ; Chapman, Mark ; Gao, Jianjiong ; Koh, Chuan Hock ; Foisy, Sylvain ; Holland, Richard ; Rimsa, Gediminas ; Heuer, Michael L. ; Brandstaetter-Mueller, H. ; Bourne, Philip E. ; Willis, Scooter. / BioJava : an open-source framework for bioinformatics in 2012. In: Bioinformatics. 2012 ; Vol. 28, No. 20. pp. 2693-2695.
    @article{ee70b9ddc78c4c408166df52fe84d826,
    title = "BioJava: an open-source framework for bioinformatics in 2012",
    abstract = "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.",
    author = "Andreas Prlic and Andrew Yates and Bliven, {Spencer E.} and Rose, {Peter W.} and Julius Jacobsen and Troshin, {Peter V.} and Mark Chapman and Jianjiong Gao and Koh, {Chuan Hock} and Sylvain Foisy and Richard Holland and Gediminas Rimsa and Heuer, {Michael L.} and H. Brandstaetter-Mueller and Bourne, {Philip E.} and Scooter Willis",
    year = "2012",
    doi = "10.1093/bioinformatics/bts494",
    language = "English",
    volume = "28",
    pages = "2693--2695",
    journal = "Bioinformatics",
    issn = "1367-4803",
    publisher = "Oxford University Press",
    number = "20",

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    Prlic, A, Yates, A, Bliven, SE, Rose, PW, Jacobsen, J, Troshin, PV, Chapman, M, Gao, J, Koh, CH, Foisy, S, Holland, R, Rimsa, G, Heuer, ML, Brandstaetter-Mueller, H, Bourne, PE & Willis, S 2012, 'BioJava: an open-source framework for bioinformatics in 2012', Bioinformatics, vol. 28, no. 20, pp. 2693-2695. https://doi.org/10.1093/bioinformatics/bts494

    BioJava : an open-source framework for bioinformatics in 2012. / Prlic, Andreas; Yates, Andrew; Bliven, Spencer E.; Rose, Peter W.; Jacobsen, Julius; Troshin, Peter V.; Chapman, Mark; Gao, Jianjiong; Koh, Chuan Hock; Foisy, Sylvain; Holland, Richard; Rimsa, Gediminas; Heuer, Michael L.; Brandstaetter-Mueller, H.; Bourne, Philip E.; Willis, Scooter.

    In: Bioinformatics, Vol. 28, No. 20, 2012, p. 2693-2695.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - BioJava

    T2 - an open-source framework for bioinformatics in 2012

    AU - Prlic, Andreas

    AU - Yates, Andrew

    AU - Bliven, Spencer E.

    AU - Rose, Peter W.

    AU - Jacobsen, Julius

    AU - Troshin, Peter V.

    AU - Chapman, Mark

    AU - Gao, Jianjiong

    AU - Koh, Chuan Hock

    AU - Foisy, Sylvain

    AU - Holland, Richard

    AU - Rimsa, Gediminas

    AU - Heuer, Michael L.

    AU - Brandstaetter-Mueller, H.

    AU - Bourne, Philip E.

    AU - Willis, Scooter

    PY - 2012

    Y1 - 2012

    N2 - 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.

    AB - 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.

    U2 - 10.1093/bioinformatics/bts494

    DO - 10.1093/bioinformatics/bts494

    M3 - Article

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    SP - 2693

    EP - 2695

    JO - Bioinformatics

    JF - Bioinformatics

    SN - 1367-4803

    IS - 20

    ER -

    Prlic A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV et al. BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics. 2012;28(20):2693-2695. https://doi.org/10.1093/bioinformatics/bts494