[Gmod-help] RE: [Gmod-gbrowse] help with the Admin tutorial

[Jayararaman, Pushkala]

Hi I would like to confirm something from the Admin tutorial: the line below:

"Copy volvox2b.gff3 into the databases/volvox folder."
from the file:
gbrowse2/tutorial/tutorial.html#data_file

I am not able to find this gff3 file in the /tutorials/database folder.
Is this the same file as the "volvox_geneproducts.gff3"?

Thanks, 
Pushkala

-----Original Message-----
From: gmodhelp at googlemail.com on behalf of Dave Clements, GMOD Help Desk
Sent: Fri 3/5/2010 3:09 PM
To: Jayararaman, Pushkala
Cc: GMOD_GBROWSE
Subject: Re: [Gmod-gbrowse] help with the Admin tutorial
 
Hi Pushkala,

I'm not sure why this is happening, but one possible cause is that since
these features are now defined in two files (volvox_geneproducts.gff3,
and volvox_geneproducts_mod.gff3)
that GBrowse is getting confused by the duplicate definitions.

Dave C.

On Tue, Mar 2, 2010 at 7:14 AM, Jayararaman, Pushkala <pjayaraman at mcw.edu>wrote:

>  I have a question referring to this paragraph on the Administrator
> tutorial:
>
> ===============================================================================================
> Another way to approach this is to make liberal use of the Alias attribute.
> For example:
>
>     ctgA example remark                             1000 2000 . . .
> Name=Remark:HGA;Alias=hga
>     ctgA example protein_coding_primary_transcript  1100 2000 . + .
> Name=Gene:hga;Alias=hga
>     ctgA example polypeptide                        1200 1900 . + .
> Name=Protein:HGA;Alias=hga
>     ctgA example protein_coding_primary_transcript  1600 3000 . - .
> Name=Gene:hgb;Alias=hgb
>     ctgA example polypeptide                        1800 2900 . - .
> Name=Protein:HGB;Alias=hgb
>
> This assigns the alias of "hga" to each of the three HGA features, and an
> alias of "hgb" to each of the two HGB features. This keeps the identities of
> these features distinct so that you can find particular ones by typing in
> the fully qualified name ("Gene:hga"), but find all candidates when you type
> in the unqualified name. For instance, when you search with "hga", GBrowse
> will now offer you three matches:
>
>
>
> (Refer Figure 5: Searching for aliases)
>
> To try this out, simply open the installed volvox2b.gff3 file with a text
> editor and edit it to match the example above.
>
> Note: GBrowse caches track images for performance reasons. If you make some
> changes to the data or config files and don't get the expected behavior, try
> turning off caching by going to the Preferences link, and turning off the
> checkbox marked "Cache tracks."
>
> ======================================================================================================
>
> This feature (where the search results are shown on the chromosomal region)
> only seems to work for Alias=hgb in the file "volvox_geneproducts_mod.gff3"
> but when I modify the gff3 file such that the remark line shows the 9th
> column to be Name=HG
> and then use the Alias=hga on the other rows except the first (as in
> volvox_geneproducts.gff3) I do not get the result on a chromosomal region,
> but all the search hits are shown highlighted on the page.
>
> The two conf files are attached herewith for clarity.
>
>
>
> ------------------------------volvox_geneproducts.gff3-------------------------------
> ##gff-version 3
> ##Note: See http://song.sourceforge.net
>
> # file: volvox_geneproducts.gff3
> ctgA    example remark  1000    2000    .       .       .       Name=HG
> ctgA    example protein_coding_primary_transcript       1100    2000
> .       +       .       Name=Gene:hga;Alias=hga
> ctgA    example polypeptide     1200    1900    .       +       .
> Name=Protein:HGA;Alias=hga
> ctgA    example protein_coding_primary_transcript       1600    3000
> .       -       .       Name=Gene:hgb;Alias=hgb
> ctgA    example polypeptide     1800    2900    .       -       .
> Name=Protein:HGB;Alias=hgb
>
> ------------------------------------------------------------------------------------------------------------
>
>
>
>
> ---------------------------------volvox_geneproducts_mod.gff3--------------------------------------
> ##gff-version 3
> ##Note: See http://song.sourceforge.net
>
> # file: volvox_geneproducts.gff3
> ctgA    example remark  1000    2000    .       .       .
> Name=HGA;Alias=hga
> ctgA    example protein_coding_primary_transcript       1100    2000
> .       +       .       Name=Gene:hga;Alias=hga
> ctgA    example polypeptide     1200    1900    .       +       .
> Name=Protein:HGA;Alias=hga
> ctgA    example protein_coding_primary_transcript       1600    3000
> .       -       .       Name=Gene:hgb;Alias=hgb
> ctgA    example polypeptide     1800    2900    .       -       .
> Name=Protein:HGB;Alias=hgb
>
> --------------------------------------------------------------------------------------------------------
>
> Please help..
>
>
> Pushkala
>
>
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