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