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

[Jeltje van Baren]

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
>
>
>
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