[Jalview-discuss] Re: Problems with alignment

[James Procter]

Hello Shanuki - it sounds like you are experiencing network problems -
either the Jalview Web services are not accessible from your local
network in York, or your computer's firewall is misconfigured.

Can you open these URLs in your web browser ?

http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS

This should have a simple HTML page returned.

http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS

A similar simple HTML page should be returned.

http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry?method=getServices

A page containing XML should be returned.

If all the above work with your web browser then you probably have
firewall issues - you will need to allow the Jalview application access
to the network (often this means adding the java executable to the list
of exceptions - programs that are allowed full access to the internet).
If you don't know how to do this then contact your local network
support, and show them this email.

All the best - happy Jalviewing!
Jim.

ish500 at york.ac.uk wrote:
> Hi, I'm running jaliview on commmand line(linux system)and trying to
> align 320 protein se4quences. Since yesterday afternoon I have trying to
> align my protein sequences using options the webservice menu(Muscle
> Multiple Sequence alignment, MAFFT Multiple Sequence Alignment, ClustalW
> Multiple Sequence Alignment). 


Today morning I tried MAFFT Multiple
> Sequence Alignment, ClustalW Multiple Sequence Alignment and keeps
> giving the same error message.ON command lines it says : MAFFT Multiple
> Sequence AlignmentClient: Failed to submit the sequences for alignment
> (probably a server side problem) When contacting
> Server:http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS
> java.net.ConnectException: Connection timed out
> 
> ClustalW Multiple Sequence AlignmentClient: Failed to submit the
> sequences for a lignment (probably a server side problem) When
> contacting
> Server:http://www.compbio.dundee.ac.uk/JalviewWS/services/Clusta lWS
> java.net.ConnectException: Connection timed out
> 
> Is there any other way i could align my sequences on jaliview?
> Thanking you,
> Shanuki
> 

-- 
-------------------------------------------------------------------
J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.