[Gmod-help] Re: [Gmod-gbrowse] GBrowse track on the fly

[Alper Yilmaz]

Hi Taner,

Thanks for your help. I hope I can implement that feature by using the
examples and help page you provided. I'll be paying a visit to
MaizeGDB next week, let me see if it's possible to meet Carson
personally, that might help tremendously.

Thanks for your help again.

alper




On Mon, Sep 21, 2009 at 10:16 AM, Taner Z. Sen <taner at iastate.edu> wrote:
> Hi Alper,
>
> At MaizeGDB, Carson Andorf wrote the code to create dynamic "custom" tracks
> to show the BLAST results mapped to the maize genome. We basically harness
> "adding annotations" feature (
> http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-Browser/htdocs/annotation_help.html
> ) and then call the file using the HTTP POST method. Here are the details:
>
> For example, for this BLAST results file that is dynamically
> generated
> (
>
> www.maizegdb.org/bhits/blasthit20090921080616.txt ), the php code that
> processes is  this:
> http://www.maizegdb.org/addblastGB.php?urlname=http://www.maizegdb.org/bhits/blasthit20090921080616.txt
>   And then the track appears as the last track on the genome browser.
>
> As an alternative, you can also create DAS tracks and serve the tracks from
> another server.
>
> Taner Sen
>
>
> At 06:01 PM 9/16/2009, Dave Clements, GMOD Help Desk wrote:
>
> Hi Alper,
>
> I apologize for the delayed response.   Your question came out right
> before I went on holiday and then I missed it when I got back.
>
> It is possible to dynamically generate GBrowse config files on the fly
> because the modENCODE project does it.  I believe that Nicole
> Washington talked briefly about this at the January 2009 GMOD meeting
> (but my notes are woefully lacking in details).
>
> Does anyone from modENCODE have an opinion on Alper's proposal?  Is it
> feasible, and if so, any ideas how?
>
> Thanks,
>
> Dave C
>
> On Thu, Aug 27, 2009 at 9:52 AM, Alper Yilmaz <alperyilmaz at gmail.com> wrote:
>> Hi all,
>>
>> In case you're interested why I need to generate a track on the fly,
>> let me briefly explain the data I would like to show as a track. We
>> calculated frequencies of words (DNA sequences from length 5 to 20) in
>> different sets (UTR, intron, upstream 3k, etc) in order to report
>> over- or under-represented words.
>> While we provide statistics about the word the researcher is inquiring
>> about, as an option, we want to provide a link "View locations of word
>> NNNNN" and when clicked, it will show the track specific to locations
>> of the selected word.
>>
>> Now, gbrowse configuration file allows defining tracks that would be
>> available to show. Since number of all possible words is vast, it's
>> not feasible to define all possible tracks in the configuration file.
>> Instead, I would like to pull genomic coordinates of selected word
>> from MySQL database and after converting that information into
>> sequence object, provide to GBrowse. Is this possible, if yes, would
>> you mind guiding me ?
>>
>> One other option might be uploading all information in GFF format
>> Bio::DB::SeqFeature::Store, but I don't know it this is feasible..
>>
>> thanks,
>> Alper Yilmaz
>>
>>
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>
>
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> Taner Z. Sen, Ph.D.
> Computational Biologist, USDA-ARS, MaizeGDB
> Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
> Iowa State University
> 1025 Crop Genome Informatics Lab
> Ames, IA 50011
> Phone: (515) 294-5326
> Fax: (515) 294-8280
> taner at iastate. edu
> http://www.public.iastate.edu/~taner/