[Gmod-help] general questions about data querying

[Ryan Golhar]

Hi Dave.  Thanks for the response.

I guess my problem comes down to "I know what I'm looking for", now I 
need to scan through the coordinates of the genes to find the ones that 
overlap.  I figured I could readily query the database the same way 
Gbrowse does to get at the data, is that a correct approach?  I suppose 
querying the database is a better solution than querying GBrowse as 
Gbrowse is just displaying the data from the database, correct?

If I load the data into Chado (I currently have it in GFF in mySQL), 
then how to I query the database?

Once I have all the data processed, I will end up creating a gff file 
and displaying it in GBrowse, but I need to get the data first...

Ryan


Dave Clements, GMOD Help Desk wrote:
> 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
>>
> 
> 
>