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

[Jeltje van Baren]

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).
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.

-Jeltje


> Hi Jeltje,
>
> Can you try searching for mRNA:CG11372.a and see if that works?  If
> so, you just need to add mRNA to your automatic classes line in the
> conf file.
>
> Scott


Josh Goodman wrote:
> Hi Dave,
>
> Can you tell me what you were searching for because I don't see this problem on FlyBase?  Using an
> ID, Name, or Alias turns up the correct hit as far as I can tell.  If you were using 'CG11372.a'
> then that is expected because that isn't a valid FlyBase ID, symbol, or synonym.
>
> Thanks,
> Josh
>
> Dave Clements, GMOD Help Desk wrote:
>   
>> Hi Jeltje,
>>
>> I don't see any problem with your configuration or the data file, and
>> I have the same interpretation of the tutorial as you do.
>>
>> Which means, um, that I don't have any idea what is wrong.
>>
>> I can tell you that the GBrowse installation at FlyBase appears to
>> have the same problem.  You can't search on mRNA names there either.
>> I suspect that this is a GBrowse problem rather than a configuration
>> or data problem.
>>
>> Does anyone else have any insight on this?
>>
>> Thanks,
>>
>> Dave C.
>> GMOD Help Desk
>>
>> On Wed, Sep 10, 2008 at 11:08 PM, Jeltje van Baren <jeltje at wustl.edu> wrote:
>>     
>>> Hey all
>>>
>>> According to the tutorial, anything that has a Name or Alias attribute in
>>> the GFF3 file can be searched for by name. However, this is not the behavior
>>> I see.
>>> I can search by gene name, but not my mRNA ID or Name.
>>> This is a sample of my GFF3:
>>>
>>> 2L      MBannot5        gene    72388   76206   0       +       .
>>> ID=CG11372;Name=CG11372
>>> 2L      MBannot5        mRNA    72388   76203   1       +       .
>>> ID=CG11372.a;Parent=CG11372;Name=CG11372.a
>>> 2L      MBannot5        exon    72388   72977   1       +       .
>>> Parent=CG11372.a
>>> 2L      MBannot5        exon    74903   75018   1       +       .
>>> Parent=CG11372.a
>>> 2L      MBannot5        exon    75078   76203   1       +       .
>>> Parent=CG11372.a
>>> 2L      MBannot5        five_prime_UTR  72388   72602   1       +
>>> 0       Parent=CG11372.a
>>> 2L      MBannot5        start_codon     72603   72605   1       +
>>> 0       Parent=CG11372.a
>>> 2L      MBannot5        CDS     72603   72977   1       +       0
>>> Parent=CG11372.a
>>> 2L      MBannot5        CDS     74903   75018   1       +       0
>>> Parent=CG11372.a
>>> 2L      MBannot5        CDS     75078   76098   1       +       1
>>> Parent=CG11372.a
>>> 2L      MBannot5        stop_codon      76096   76098   1       +
>>> 0       Parent=CG11372.a
>>> 2L      MBannot5        three_prime_UTR 76099   76203   1       +
>>> 0       Parent=CG11372.a
>>>
>>> I can type CG11372 in the Search box, and then all transcripts are
>>> highlighted. Searching for CG11372.a results in a "The landmark named
>>> CG9171.a is not recognized." message.
>>> I tried prefixing with the Source name (MBannot5) and the Track ID (MB5),
>>> like so: MB5:CG9171.a (I seem to remember one of these used to be possible)
>>> but that doesn't work.
>>> I also tried adding ID and Name to 'search attributes' in the config file,
>>> but to no avail.
>>> I'm running the stable 1.69 version.
>>>
>>> You can find the gbrowser at
>>> http://mblab.wustl.edu/cgi-bin/gbrowse/fly5/
>>> and the config file at
>>> http://mblab.wustl.edu/~jeltje/fly5.conf
>>>
>>> What am I missing?
>>>
>>> -Jeltje
>>>
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>>>       
>>
>>     
>
>
>   
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