[Gmod-help] RE: [Gmod-gbrowse] Gbrowse2 - Invoking URLs to view blast HSPs

[Naveed Ishaque (TSL)]

Hi Dave,

I add the following code to the URL of our genome browser - "?add=SuperContig0+blast_hit+example1+271700..272000". I've tried it out with some gbrowse 1.x servers at the ?add=... code works fine. 

Whenever we try the code we get a 500 Internal server error. Whenever I replace the "?add" with "?name" (?name=SuperContig0:271700..272000) it shows the selected region.

Could this be due to having an earlier version of gbrowse2?

Thanks,

Nav

-----Original Message-----
From: gmodhelp at googlemail.com [mailto:gmodhelp at googlemail.com] On Behalf Of Dave Clements, GMOD Help Desk
Sent: 11 February 2010 23:49
To: Naveed Ishaque (TSL)
Cc: gmod-gbrowse at lists.sourceforge.net
Subject: Re: [Gmod-gbrowse] Gbrowse2 - Invoking URLs to view blast HSPs

Dear Nav,

I don't think this functionality was supposed to go away in GBrowse 2.

Can you send the exact URL you are using?  This will help with debugging.

Thanks,

Dave C.

On Tue, Feb 9, 2010 at 9:09 AM, Naveed Ishaque (TSL)
<Naveed.Ishaque at sainsbury-laboratory.ac.uk> wrote:
> Dear all,
>
>
>
> I would like to be able to display blast hits on gbrowse2 session. With
> gbrowse1.x I have been successful in using the "?add=..." (as in the Invoking
> URL section of the gbrowse HOWTO) parameter to display the HSPs but cannot
> use the same code with gbrowse2. Other URL invoking features like h_region
> seem to work and I'm wondering if I'm doing anything wrong.
>
>
>
> Also, would you recommend any other ways of displaying blast results onto
> gbrowse2? My current work flow is to perform a blast search on a server and
> generating a HTML file displaying the results which will contain links to
> the genome browser displaying the HSP as an "?add=..." parameter in the URL.
>
>
>
> Thanks,
>
>
>
> Nav
>
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