[Jalview-discuss] question about using DAS service and JalviewLite

[Jim Procter]

On 10/03/2010 04:45, Sai Tong wrote:
> So from what I understand, there is no way one can pass-on uniprot id
> directly into JalviewLite (applet version of Jalview) to  search uniport
> and retrieve protein sequence and sequence feature annotations, similar
> to what one can do using the standalone version of  Jalview. Is that
> correct ?
>    
It is.
>    in order to add feature annotations to JalviewLite , one needs to
> first create a gff file containing the feature annotation and then use
> the following:
>
>   <param name="Features" value="file.gff">
>
> in order to make the features annotated and visualizable inside
> JalviewLite .  What other ways that one can add feature annotations via
> the use of JalviewLite applet.
>    
Sequence features can be imported using the Jalview feature file or GFF 
files - and the ordering and colouring of the features are controlled 
using the feature colourscheme definitions (see the jalview feature file 
format http://www.jalview.org/help/html/features/featuresFormat.html ).

The 2.4 version of JalviewLite has no specific features for database 
querying - this is because its designed as a web app user interface 
component, so its restricted to the browser's sandbox (and cannot query 
arbitrary URLs). However, its relatively straightforward to set up a 
server-side service that the applet could use to retrieve a gff or 
Jalview features file containing alignment annotation.

All you need to do is put the URL of the service in the value field of 
the 'Features' parameter. You can also upload and control the display of 
features via javascript - check out the example and API for details 
(http://www.jalview.org/examples/formComplete.html - scroll to the 
bottom of the page).

One development path for JalviewLite is to introduce some components 
that people can use on their servers to more tightly integrate the 
applet with their own web services. For instance, the DASTY server side 
DAS proxy system could be used by JalviewLite, with only a few 
modifications. Let me know if your interested in this.

Thanks for the email, and please get in contact if your interested in 
extending what JalviewLite can do for your application!

Jim.

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J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
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