[Gmod-help] Re: [Gmod-gbrowse] Search on mRNA ID

[Scott Cain]

As much as I would like a simple solution (like GBrowse not supporting
it), I just did a simple test with the yeast chromosome 1&2 database
and changes some of the ids and names to contain periods and searching
still worked.  What I think Victor may be remembering is that you
cannot have a colon in the name, as that does invoke a reserved syntax
of "type:name".

Unfortunately, I'm no closer to figuring it out though.

Scott


On Thu, Sep 11, 2008 at 5:11 PM, Jeltje van Baren <jeltje at wustl.edu> wrote:
> Thanks Victor!
>
> While I'm glad to have a solution for this, I think it's probably better if
> GBrowse just allowed periods in its search.
> Otherwise this issue is going to come up again and again with new users,
> since lots of people use periods when naming transcripts of a gene.
>
> -Jeltje
>
>
> Victor wrote:
>
> At 12:44 PM 9/11/2008, Jeltje van Baren wrote:
>
> Hi Scott and Josh
>
> I tried mRNA:CG11372.a and that doesn't work either (you can try for
> yourself at
> <http://mblab.wustl.edu/cgi-bin/gbrowse/fly5>http://mblab.wustl.edu/cgi-bin/gbrowse/fly5).
> I did add mRNA to the automatic classes, but that doesn't help.
>
> CG11372.a is a correct ID in MB5, the track I that's shown on this browser.
> The corresponding FlyBase gene is CG11372-RA.
>
> A had a lot of trouble with IDs and names which
> were including dots - when you submit it for a search,
> GBrowse was assuming that dot means that you submit
> something like 'method.source' combo (in terms of GFF2).
> So we just agreed to avoid use of such stuff at FlyBase
> and you can notice that we use dashes instead (CG11372-RA).
> Maybe this problem can be somehow avoided or bypassed, but
> it is simpler not to use risky syntax - saves a lot of time..
> And I don't remember what I found at the time after debugging -
> it could be not GBrowse per se, but something from BioPerl.
>
> V. Strelets
> FlyBase Consortium
>
>
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory