[Gmod-help] general questions about data querying

[Dave Clements, GMOD Help Desk]

Hi Ryan,

I'm CC'ing the GBrowse list as I often get questions like this at
conferences.  I think this is worth a general discussion.

There are a couple of widely used mechanisms for locating information
in GBrowse: coordinates, names, BLAST.  GBrowse does not have a
mechanism for asking "Show me other regions that look like this
region", where "look like" is determined at run time based on
displayed features in the selected region.  That would be ideal, but
as you can imagine, it would also be a *lot* of work requiring both
research and coding.  (Anyone out there need to do a thesis?)

The next best thing is for sites to define their own set of
interesting questions and run some preprocessing on the data to find
regions that are "interesting".  There are several ways to display
and/or link to interesting regions.  There could be a separate page
that lists them; on any feature that is interesting the popup/hover
could have a link to "show other +/- strand overlapping genes".  If
there aren't too many of them you could have a track in the overview
or region areas that shows the interesting areas and then users could
zoom in on them.


Hmm.  I just reread your email, and you *might* be asking a different
question.  Do you want to ask this question in the database itself,
rather than in GBrowse?  To do this, I would load the data into Chado
and ask it there.  The databases that usually back GBrowse are built
for speed, rather than for clarity and ad hoc questions.


Hopefully, I answered your question, and your next question too.  ;-)

I also encourage anyone else on the list to respond.

Dave C.


On Wed, Nov 11, 2009 at 12:42 PM, Ryan Golhar <golharam at umdnj.edu> wrote:
> Hi,
>
> I recently installed Gbrowse to view some data I have, but now I'm
> interested in performing a more thorough analysis of the data.  I want to
> identify certain regions of the genome that contain overlapping genes  on
> the plus/minus strand ie one gene on the plus strand and a 2nd gene on the
> minus strand overlapping the 1st gene.
>
> I can see one or two of these occurrences in GBrowse, but I don't want to do
> this manually.  Is there a way to query the database to find all occurrences
> of these?
>
> Ryan
>



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