[Gmod-help] polypeptide view in Gbrowse

[Lincoln Stein]

Hi Newton,

Have you tried passing the draw_protein option?

 [Polypeptide]
 feature = polypeptide
 glyph   = transcript
 draw_protein = 1

Also check out the "protein" and "translation" glyphs.

The T. cruzi problem sounds like a chado issue -- I will defer to Scott
and/or David on this.

Best,

Lincoln

On Tue, Dec 16, 2008 at 2:01 PM, Newton Vidal <nwvidal at gmail.com> wrote:

> Dear all,
>
> I am starting to work with GMOD and Chado, and I have uploaded genbank
> files from five different protozoan genomes, using bp_genbank2gff3.pl and
> gmod_bulk_load_gff3.pl scripts in our local chado v. 1.0 database.
>
> I have run into two major problems when visualizing data with Gbrowse v.
> 1.69:
>
> ·        The polypeptide feature shows nucleic acid sequence instead of
> amino acid, when clicked;
> ·        For four of the genomes (Leishmania sp. and Trypanosoma brucei)
> the others features work fine, but for T. cruzi, no data is provided when I
> click its features.
>
> I have edited chado.conf file to work with my database and added the lines
> below:
>
> [Polypeptide]
> feature      = polypeptide
> glyph        = transcript
> height       = 10
> key          = Polypeptide
> bgcolor      = green
>
> I'm sending attached T. brucei and T. cruzi's GFF files and gbrowse conf
> file. I have a 80MB dump file and I can share it if needed.
>
> Thanks in advance,
>
> Newton Vidal
>



-- 
Lincoln D. Stein

Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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