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

[Josh Goodman]

Ah ok.  It looks like the search is case sensitive for these items whereas it isn't for other
objects (e.g. gene symbols).  I'll pass this along to Victor.

Thanks,
Josh

Dave Clements, GMOD Help Desk wrote:
> Hi Josh,
> 
> I went to flybase and took a transcript name from a GBrowse display:
> cnn-rd.  This is shown with the CNN gene.
> 
> Dave C
> 
> On Thu, Sep 11, 2008 at 4:50 PM, Josh Goodman <jogoodma at indiana.edu> 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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>>>
>>>
> 
> 
>