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

[Andrew Waterhouse]

Hello Sai,

The reason JalviewLite cannot search and retrieve uniprot sequences 
directly is due to the security of web browsers, ie a page cannot run 
scripts that access files that come from a different server without the 
users permission.

When you start up the Jaliew standalone version, you agreed to allow the 
program to access other web servers, so the program connects to many DAS 
servers around the world.

The applet in Jalview 2 was designed to be dropped into any web page 
anywhere for easy use by researchers. In order to access other servers, 
such as Uniprot, then an amount of coding is required, and this would 
reduce the portability of the applet.

I would suggest a jQuery JalivewLite plugin would be very useful for 
javascript web developers, for sequence/feature retrieval from DAS 
servers. However, this would still require the coder to do some server 
side coding (a proxy server would be the easiest solution)


Would this be a good project for "Google Summer of Code" Jim?


Andrew Waterhouse




Jim Procter wrote:
> 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.
>
> -------------------------------------------------------------------
> J. B. Procter  (JALVIEW/ENFIN)  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.
>
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