[ensembl-dev] [SPAM] - Re: Browser query - Email found in subject

Oliver, Gavin gavin.oliver at almacgroup.com
Thu Nov 4 17:22:41 GMT 2010


Thanks for the advice - I'll have to look into this in a bit more detail
and figure out what works best.

Best, 

Gavin

-----Original Message-----
From: Andy Jenkinson [mailto:andy.jenkinson at ebi.ac.uk] 
Sent: 03 November 2010 17:33
To: Maximilian Haussler
Cc: Oliver, Gavin; dev at ensembl.org
Subject: [SPAM] - Re: [ensembl-dev] Browser query - Email found in
subject

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
> 
>  
>  
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