JABAWS 2

JABAWS^2.0:Disorder is free software which provides web services for prediction of protein disorder, multiple sequence alignment and amino acid conservation conveniently packaged to run on your local computer, server or cluster. Disorder prediction services are based on DisEMBL, IUPred, Ronn, GlobPlot, conservation is calculated by AACon, multiple sequence alignment services are the Clustal Omega, Clustal W, JABAWS is free software which provides web services for multiple sequence alignment, prediction of protein disorder, and amino acid conservation conveniently packaged to run on your local computer, server or cluster. JABAWS v2.0 introduces protein disorder prediction services based on DisEMBL, IUPred, Ronn, GlobPlot and protein sequence alignment conservation measures calculated by AACon. A new multiple sequence alignment service for Clustal Omega is also provided, in addition to standard JABAWS:MSA services for Clustal W, MAFFT, MUSCLE, TCOFFEE and PROBCONS. -JABA Web Services can be accessed from the Jalview multiple sequence alignment editor and analysis workbench to allow multiple alignment calculations limited only by your own local computing resources.

- +JABA Web Services can be accessed from the Jalview desktop application and provide multiple alignment and sequence analysis calculations limited only by your own local computing resources.
+
+Please note that JABAWS 2 is supported by Jalview 2.6.1 onwards, but the disorder prediction, Clustal Omega and AACon services will only be accessible in Jalview 2.8 (due for release in January 2012). In the meantime you can access all JABAWS2 services through the JABAWS command-line client.

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For Bioinformaticians/Developers

The Server: JABAWS Web Application aRchive (55M) +"http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive (55M)
The Client: - Command Line Client binary | source + Command Line Client binary | source @@ -92,22 +98,22 @@ Check out the quick start guide for furt

Public JABAWS Server

You can access our public JABA Web Services with our command line client, Jalview, or with your own program. Jalview is configured to use this public JABAWS server by default.

You can access our public JABA Web Services with our command line client, Jalview, or with your own program. Jalview version 2.8 or later is fully compatible with JABAWS 2. The latest versions of Jalview are configured to use public JABAWS server by default.

The JABAWS public web services address is http://www.compbio.dundee.ac.uk/jabaws
A detailed web services description is available from here: WSDL List

These web services will reject submissions containing more then one thousand sequences. Should you find this to be insufficient for your needs, or if you are concerned about privacy or on an unreliable network connection, then you can download and run the JABAWS Server on your own hardware.

- - +

These web services accept submissions of less than one thousand sequences. Should you find this to be insufficient for your needs, or if you are concerned about privacy or on an unreliable network connection, then you can download and run the JABAWS Server on your own hardware.

Previous versions of JABAWS

JABAWS 1 is available from here http://www.compbio.dundee.ac.uk/jabaws1. We advise you to update to the JABAWS 2 as this version is fully backward compatible with JABAWS 1 and contain numerous improvements. Please consult the manual for more information on versions compatibility.

Reference

Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MSA" Bioinformatics 2011; doi: 10.1093/bioinformatics/btr304.

Last update: 16 September 2011
+

Last update: 10 December 2011
This site is best viewed in Firefox 3.6, Google Chrome 10, Internet Explorer 8 or above

For Users

- The Server: JABAWS Virtual Appliance: (520M) + The Server: JABAWS Virtual Appliance: (520M) or use JABAWS on Amazon Webservices Cloud
The Client: Jalview (18M)

To use JABA Web Services on most operating systems, just download and install the JABAWS Virtual Appliance (VA) or even easier - just start JABAWS machine on the cloud and point Jalview at it!

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For System Administrators

The Server: JABAWS Web Application aRchive (55M)

+"http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive (55M)

JABAWS requires a Servlet 2.4 compatible servlet container like Apache-Tomcat to run. Please check the quick start guide for installation instructions.