JABAWS 3 (alpha version)
-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 v3.0a 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 desktop application and provide multiple alignment and sequence analysis calculations limited only by your own local computing resources.
-
-Please note that JABAWS 3a 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 JABAWS3 services through the JABAWS command-line client.
JABAWS 2.1
++JABAWS +is free software which provides web services conveniently +packaged to run on your local computer, server, cluster or Amazon EC2 instance. +
+ +Services for multiple sequence alignment include +Clustal Omega, +Clustal W, +MAFFT, +MUSCLE, +T-Coffee, +ProbCons, +MSAProbs, and +GLProbs. +Analysis services allow prediction of the protein secondary structure with +Jpred and protein disorder with +DisEMBL, +IUPred, +Jronn (a Java implementation of Ronn by P. Troshin and G. Barton, unpublished), and +GlobPlot; and calculation of amino acid alignment conservation +with AACon. +The secondary structure for an RNA aligment can be predicted with the RNAalifold program from the +Vienna RNA package. +
+ +
+JABAWS 2.1 installation can be accessed from the Jalview desktop
+application (version 2.8 onwards) and the JABAWS command-line client.
+JABAWS 2.1 is able to provide multiple alignment and sequence analysis calculations limited only by your own
+computing resources.
+
|
-
+ For Users
- 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! + The Server: JABAWS Virtual Appliance: (440M) + or JABAWS on Amazon Webservices Cloud+ The Main Client: Jalview (18M) + To use JABAWS 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! |
- For System Administrators
-
- The Server: 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. - |
+
- For Bioinformaticians/Developers
-The Server: JABAWS Web Application aRchive (55M)
+ For Bioinformaticians/Developers
+The Server: JABAWS Web Application aRchive (55M)
- The Client: - Command Line Client binary | source - - - - You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server. The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can just script against our public server (see below) with the command line client or you own script. + Command Line Client binary | source + + +You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server. +The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can just script against our public +server (see below) with the command line client or you own script. Check out the quick start guide for further details. - |
-
Public JABAWS Server
-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 3a. The latest versions of Jalview are configured to use public JABAWS server by default.
+You can access our public JABAWS web services with our command line client, + Jalview, or with your own program. Jalview version 2.8 or later is fully compatible with JABAWS 2.1. + 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 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.
+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.
++We advise you to update to JABAWS 2.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and contains +some important bug fixes. Please consult the manual +for more information on compatibility between versions.
Should you require them, however, old versions of JABAWS are available here:
+-
+
- http://www.compbio.dundee.ac.uk/jabaws1 +
- http://www.compbio.dundee.ac.uk/jabaws2 +
- http://www.compbio.dundee.ac.uk/jabaws201 +
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.
-