[Jalview-discuss] Upload scoring matrix (was Upload files in Jalview)

Jim Procter jprocter at compbio.dundee.ac.uk
Mon Mar 9 10:05:22 GMT 2015

Hello again, Laécio.

On 09/03/2015 03:26, Laécio Freitas Chaves wrote:
> Currently is possible change the parameters of the execution of an 
> alignment, for example, choose the substitution matrix. it is possible 
> uploading an matrix (or other file) in Web Service -> Alignment -> 
> edit settings and run?

Unfortunately, no. Alignment settings such as the substitution matrix 
parameter are defined by the service interface for the JABAWS server 
that Jalview is connected to.

 From your emails over at jabaws-discuss I gather you have set up your 
own JABAWS server - which means you could configure these settings on 
the server to allow custom substitution matrices, but they would have to 
be provided server-side rather than client side. Alternatively, you 
could consider creating a new MSA service interface that can take - in 
addition to sequences and parameters, a substitution matrix file. 
However, you'd then have to extend the existing JABAWS client library 
(and Jalview) in order to to allow Jalview to use the new interface.

Happy to talk more about this if you are interested in proceeding !

Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, College of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk
The University of Dundee is registered Scottish charity: No.SC015096

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