Java bioinformatics analysis web services for multiple sequence alignment-JABAWS:MSA

    Research output: Contribution to journalArticle

    36 Citations (Scopus)

    Abstract

    JABAWS is a web services framework that simplifies the deployment of web services for bioinformatics. JABAWS: MSA provides services for five multiple sequence alignment (MSA) methods (Probcons, T-coffee, Muscle, Mafft and ClustalW), and is the system employed by the Jalview multiple sequence analysis workbench since version 2.6. A fully functional, easy to set up server is provided as a Virtual Appliance (VA), which can be run on most operating systems that support a virtualization environment such as VMware or Oracle VirtualBox. JABAWS is also distributed as a Web Application aRchive (WAR) and can be configured to run on a single computer and/or a cluster managed by Grid Engine, LSF or other queuing systems that support DRMAA. JABAWS: MSA provides clients full access to each application's parameters, allows administrators to specify named parameter preset combinations and execution limits for each application through simple configuration files. The JABAWS command-line client allows integration of JABAWS services into conventional scripts.

    Original languageEnglish
    Pages (from-to)2001-2002
    Number of pages2
    JournalBMC Bioinformatics
    Volume27
    Issue number14
    DOIs
    Publication statusPublished - 15 Jul 2011

    Cite this

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    title = "Java bioinformatics analysis web services for multiple sequence alignment-JABAWS:MSA",
    abstract = "JABAWS is a web services framework that simplifies the deployment of web services for bioinformatics. JABAWS: MSA provides services for five multiple sequence alignment (MSA) methods (Probcons, T-coffee, Muscle, Mafft and ClustalW), and is the system employed by the Jalview multiple sequence analysis workbench since version 2.6. A fully functional, easy to set up server is provided as a Virtual Appliance (VA), which can be run on most operating systems that support a virtualization environment such as VMware or Oracle VirtualBox. JABAWS is also distributed as a Web Application aRchive (WAR) and can be configured to run on a single computer and/or a cluster managed by Grid Engine, LSF or other queuing systems that support DRMAA. JABAWS: MSA provides clients full access to each application's parameters, allows administrators to specify named parameter preset combinations and execution limits for each application through simple configuration files. The JABAWS command-line client allows integration of JABAWS services into conventional scripts.",
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    Java bioinformatics analysis web services for multiple sequence alignment-JABAWS:MSA. / Troshin, Peter V.; Procter, James B.; Barton, Geoffrey J.

    In: BMC Bioinformatics, Vol. 27, No. 14, 15.07.2011, p. 2001-2002.

    Research output: Contribution to journalArticle

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