[ensembl-dev] Browser query

[Andy Jenkinson]

Hi Gavin,

As far as I know it's not possible to highlight a region directly via a link.

However, as Max says, attaching a DAS track via a link is an alternative option. The "specifying some sort of ID to the track name which will trigger the highlighting" bit would be quite complicated and might not be feasible, but depending on the sparsity of the regions of interest might not be necessary. Instead you could just create a single DAS track containing all regions of interest. Each ROI can be displayed as a glyph of your choice (e.g. a box, arrows, lines, etc) to indicate the location of the ROI in the genome. The advantage being that the user can see all the regions of interest as they browse.

A simpler version of the above if you only have a few ROIs would be to host a file (e.g. GFF) containing them. Ensembl can download it on the fly for each request, and you can activate this via a link just as you can for DAS tracks.

You may wish these documents:
http://www.ensembl.org/info/website/upload/index.html
http://www.ensembl.org/info/docs/webcode/linking.html

Cheers,
Andy

On 3 Nov 2010, at 16:53, Maximilian Haussler wrote:

> You can write your own DAS server, then add parameters to attach this DAS server to the URL, specifying some sort of ID to the track name which will trigger the highlighting when the DAS server sees it.
> 
> Not really easy to implement, but possible. I've done something similar recently. 
> 
> I wonder if there is a simpler way...
> 
> cheers
> Max
> 
> On Wed, Nov 3, 2010 at 11:08 AM, Oliver, Gavin <gavin.oliver at almacgroup.com> wrote:
> Hi all,
> 
>  
> I am trying to link via a simple URL from an internal webpage to the Ensembl genome browser.  I want to be able to link to a given chromosomal region.  This is not a problem.  What I am wondering is whether there is any way of ‘highlighting’ my region of interest.
> 
>  
> For example if I am interested in human chromosome X bases 50-100, I would like to show bases 1 – 150 but have 50-100 highlighted in some manner (similar to how a blast result is shown in the browser as a red bar).
> 
>  
> Is this possible or am I pushing my luck?
> 
>  
> Best,
> 
> Gavin
> 
>  
>  
> 
> The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender.
> 
>  
> Almac Group (UK) Limited, registered no. NI061368.  Almac Sciences Limited, registered no. NI041550.  Almac Discovery Limited, registered no. NI046249.  Almac Pharma Services Limited, registered no. NI045055.  Almac Clinical Services Limited, registered no. NI041905.  Almac Clinical Technologies Limited, registered no. NI061202.  Almac Diagnostics Limited, registered no. NI043067.  All preceding companies are registered in Northern Ireland with a registered office address of Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK.  
> 
>  
> Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034.
> 
>  
> Almac Clinical Services LLC, Almac Clinical Technologies LLC and Almac Diagnostics LLC are Delaware limited liability companies and Almac Group Incorporated is a Delaware Corporation.  More information on the Almac Group can be found on the Almac website: www.almacgroup.com
> 
> 
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev
> 
> 
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev