[Gmod-help] a questions

[Zhiliang Hu]

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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