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

[Josh Goodman]

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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>>
> 
> 
>