[Gmod-help] a questions

[Zhiliang Hu]

Hi Dave,

Along the same line of questions, I wonder where can I find the (MySQL) database schema behind the GBrowse?  Also, is there a map between the database schema and the GFF fields -- it will help to understand better how things work.

I apologize if the info is already in the public domain but I just have not read thorough enough (please point it out to me :-)

Thanks,
Zhiliang


>Date: Tue, 07 Oct 2008 15:19:42 -0500
>To: help at gmod.org
>From: Zhiliang Hu <zhu at iastate.edu>
>Subject: Re: [Gmod-help] a questions
>Cc: "GMOD Help Desk" <help at gmod.org>
>
>Hi Dave,
>
>I have loaded my GBrowse (<http://www.animalgenome.org:2358/cgi-bin/gbrowse/>http://www.animalgenome.org/cgi-bin/gbrowse/) using Scott's script "load_genbank.pl" without involving GFF files. I have yet to figure out how the changes you suggested be done with the script... I am learning that the column 9 of GFF3 file can be very "information rich"! ;-)
>
>Thank you!
>
>Zhiliang
>
>
>At 10:08 AM 10/7/2008 -0700, Dave Clements, GMOD Help Desk wrote:
>>Hi Zhiliang,
>>
>>I don't know the answer to your question, but...
>>
>>How are you loading the Genbank data into GBrowse?  If you are first
>>creating a GFF3 file then you can modify the GFF3 file before loading
>>it.  In particular, I think you could leave column 1 of the GFF as
>>"NC_007299" on all the lines for chromosome 1, and change column 9 of
>>just the line that defines the chromosome from "Name=NC_007299" to
>>"Name="Chr.1"  This leaves the internal ID as NC_007299, but displays
>>it as Chr.1
>>
>>Or does this not address what you are trying to do?
>>
>>Alternatively, If you can't find any links that are broken with your
>>current approach, then you can leave it as it is.
>>
>>Hope this helps,
>>
>>Dave C.
>>
>>On Fri, Oct 3, 2008 at 12:02 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
>>> I have a technical question -- I set up my Gbrowse with Genbank files, and wish to call each chromosome by a name like "Chr.1", and tried so by changing "ACCESSION" name from "NC_007299" to "Chr.1".  It displayed alright, but just wonder if this is the right way to do?  (wonder if ACCESSION also used for other things like web links).
>>>
>>> Zhiliang
>>
>>-- 
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