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<P><FONT SIZE=2>I have managed to sort out the problem with the Admin tutorial.<BR>
Modifying the first line this way:<BR>
<BR>
ctgA example remark 1000 2000 . . . Name=Remark:HGA;Alias=hga<BR>
<BR>
This was a simple case of personal error (of my overlooking details that were explained in the Admin tutorials)<BR>
<BR>
Pushkala<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmodhelp@googlemail.com on behalf of Dave Clements, GMOD Help Desk<BR>
Sent: Fri 3/5/2010 3:09 PM<BR>
To: Jayararaman, Pushkala<BR>
Cc: GMOD_GBROWSE<BR>
Subject: Re: [Gmod-gbrowse] help with the Admin tutorial<BR>
<BR>
Hi Pushkala,<BR>
<BR>
I'm not sure why this is happening, but one possible cause is that since<BR>
these features are now defined in two files (volvox_geneproducts.gff3,<BR>
and volvox_geneproducts_mod.gff3)<BR>
that GBrowse is getting confused by the duplicate definitions.<BR>
<BR>
Dave C.<BR>
<BR>
On Tue, Mar 2, 2010 at 7:14 AM, Jayararaman, Pushkala <pjayaraman@mcw.edu>wrote:<BR>
<BR>
> I have a question referring to this paragraph on the Administrator<BR>
> tutorial:<BR>
><BR>
> ===============================================================================================<BR>
> Another way to approach this is to make liberal use of the Alias attribute.<BR>
> For example:<BR>
><BR>
> ctgA example remark 1000 2000 . . .<BR>
> Name=Remark:HGA;Alias=hga<BR>
> ctgA example protein_coding_primary_transcript 1100 2000 . + .<BR>
> Name=Gene:hga;Alias=hga<BR>
> ctgA example polypeptide 1200 1900 . + .<BR>
> Name=Protein:HGA;Alias=hga<BR>
> ctgA example protein_coding_primary_transcript 1600 3000 . - .<BR>
> Name=Gene:hgb;Alias=hgb<BR>
> ctgA example polypeptide 1800 2900 . - .<BR>
> Name=Protein:HGB;Alias=hgb<BR>
><BR>
> This assigns the alias of "hga" to each of the three HGA features, and an<BR>
> alias of "hgb" to each of the two HGB features. This keeps the identities of<BR>
> these features distinct so that you can find particular ones by typing in<BR>
> the fully qualified name ("Gene:hga"), but find all candidates when you type<BR>
> in the unqualified name. For instance, when you search with "hga", GBrowse<BR>
> will now offer you three matches:<BR>
><BR>
><BR>
><BR>
> (Refer Figure 5: Searching for aliases)<BR>
><BR>
> To try this out, simply open the installed volvox2b.gff3 file with a text<BR>
> editor and edit it to match the example above.<BR>
><BR>
> Note: GBrowse caches track images for performance reasons. If you make some<BR>
> changes to the data or config files and don't get the expected behavior, try<BR>
> turning off caching by going to the Preferences link, and turning off the<BR>
> checkbox marked "Cache tracks."<BR>
><BR>
> ======================================================================================================<BR>
><BR>
> This feature (where the search results are shown on the chromosomal region)<BR>
> only seems to work for Alias=hgb in the file "volvox_geneproducts_mod.gff3"<BR>
> but when I modify the gff3 file such that the remark line shows the 9th<BR>
> column to be Name=HG<BR>
> and then use the Alias=hga on the other rows except the first (as in<BR>
> volvox_geneproducts.gff3) I do not get the result on a chromosomal region,<BR>
> but all the search hits are shown highlighted on the page.<BR>
><BR>
> The two conf files are attached herewith for clarity.<BR>
><BR>
><BR>
><BR>
> ------------------------------volvox_geneproducts.gff3-------------------------------<BR>
> ##gff-version 3<BR>
> ##Note: See <A HREF="http://song.sourceforge.net">http://song.sourceforge.net</A><BR>
><BR>
> # file: volvox_geneproducts.gff3<BR>
> ctgA example remark 1000 2000 . . . Name=HG<BR>
> ctgA example protein_coding_primary_transcript 1100 2000<BR>
> . + . Name=Gene:hga;Alias=hga<BR>
> ctgA example polypeptide 1200 1900 . + .<BR>
> Name=Protein:HGA;Alias=hga<BR>
> ctgA example protein_coding_primary_transcript 1600 3000<BR>
> . - . Name=Gene:hgb;Alias=hgb<BR>
> ctgA example polypeptide 1800 2900 . - .<BR>
> Name=Protein:HGB;Alias=hgb<BR>
><BR>
> ------------------------------------------------------------------------------------------------------------<BR>
><BR>
><BR>
><BR>
><BR>
> ---------------------------------volvox_geneproducts_mod.gff3--------------------------------------<BR>
> ##gff-version 3<BR>
> ##Note: See <A HREF="http://song.sourceforge.net">http://song.sourceforge.net</A><BR>
><BR>
> # file: volvox_geneproducts.gff3<BR>
> ctgA example remark 1000 2000 . . .<BR>
> Name=HGA;Alias=hga<BR>
> ctgA example protein_coding_primary_transcript 1100 2000<BR>
> . + . Name=Gene:hga;Alias=hga<BR>
> ctgA example polypeptide 1200 1900 . + .<BR>
> Name=Protein:HGA;Alias=hga<BR>
> ctgA example protein_coding_primary_transcript 1600 3000<BR>
> . - . Name=Gene:hgb;Alias=hgb<BR>
> ctgA example polypeptide 1800 2900 . - .<BR>
> Name=Protein:HGB;Alias=hgb<BR>
><BR>
> --------------------------------------------------------------------------------------------------------<BR>
><BR>
> Please help..<BR>
><BR>
><BR>
> Pushkala<BR>
><BR>
><BR>
> ------------------------------------------------------------------------------<BR>
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><BR>
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