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A Practical Guide to Phylogenetics for Nonexperts
12:00

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Published on: February 5, 2014

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

Peter V Troshin1, James B Procter, Geoffrey J Barton

  • 1Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.

Bioinformatics (Oxford, England)
|May 20, 2011
PubMed
Summary
This summary is machine-generated.

JABAWS simplifies bioinformatics web service deployment with JABAWS:MSA, offering five multiple sequence alignment methods. This framework is available as a Virtual Appliance or Web Application Archive for flexible integration into various computing environments.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Web Services

Background:

  • Deploying bioinformatics web services can be complex.
  • There is a need for simplified and flexible service frameworks.

Purpose of the Study:

  • To introduce JABAWS (Java Bioinformatics Web Services) as a framework for simplifying web service deployment.
  • To present JABAWS:MSA, which integrates five multiple sequence alignment methods.

Main Methods:

  • JABAWS is provided as a Virtual Appliance (VA) for easy setup on virtualization platforms.
  • It is also distributed as a Web Application Archive (WAR) for single computer or cluster deployment.
  • A command-line client enables integration into existing scripts.

Main Results:

  • JABAWS:MSA offers services for Probcons, T-coffee, Muscle, Mafft, and ClustalW.
  • The framework allows full access to application parameters and customizable presets.
  • It supports integration with cluster queuing systems via DRMAA.

Conclusions:

  • JABAWS effectively simplifies the deployment and management of bioinformatics web services.
  • JABAWS:MSA enhances the Jalview workbench by providing access to multiple sequence alignment tools.
  • The framework's flexibility supports diverse computational environments.