[Gmod-help] polypeptide view in Gbrowse

[Newton Vidal]

Hi, Scott and Lincoln.

I have another question, related to my problem, but arising another issue:

I have configured two different glyphs, one as CDS and the other as protein.
When I zoomed in the main Gbrowse screen, the CDS glyph is shown as protein
sequence and the protein is shown as nucleotide sequence. Is this behavior
expected? Why the CDS, that codes for a protein, but is composed of DNA is
shown as protein and the protein glyph is not?

Representative pictures are attached.


Thanks in advance.

Newton.


On Tue, Dec 16, 2008 at 8:52 PM, Dave Clements, GMOD Help Desk <
gmodhelp at googlemail.com> wrote:

> Hi Newton, Scott, Lincoln,
>
> The draw_protein_target option of the segments glyph did not work as
> of October.  I don't recall any recent problems (or success either)
> with the draw_target option of the transcript glyph, although it
> wouldn't surprise me if both options use the same code.  (See
> http://thread.gmane.org/gmane.science.biology.gmod.gbrowse/808 for
> more on draw_protein_target problems).
>
> I also loaded the GFF3 file for Tcruzi into a mysql database.  I did
> not get any load errors (or Apache runtime errors), but nothing
> displays for me either.  All landmarks are unrecognized.  I tried
> playing around with the conf file but to no avail.
>
> Dave C.
>
>
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
>
>
> On Tue, Dec 16, 2008 at 1:02 PM, Scott Cain <cain.cshl at gmail.com> wrote:
> > Hi Lincoln and Newton,
> >
> > I was under the impression that the draw_protein option was
> > incompletely implemented, but if it works with other database
> > adaptors, perhaps there is a bug in the Chado GBrowse adaptor.  Have
> > you tried the cds glyph, which should display residues when zoomed in
> > far enough?  If draw_protein doesn't work but the cds glyph does, it
> > indicates a Bio::Graphics problem.  If neither work, it is more likely
> > a Chado adaptor or data problem.
> >
> > As for the T. cruzi problem--I don't see anything in the data that
> > looks problematic.  Where there any error messages while loading or in
> > the apache error_log (with a preemptive note: error messages about
> > Bio::Graphics::BrowserConfig don't mean anything)?
> >
> > Scott
> >
> >
> > On Tue, Dec 16, 2008 at 3:35 PM, Lincoln Stein <lincoln.stein at gmail.com>
> wrote:
> >> 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>
> >>
> >
> >
> >
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
> > Ontario Institute for Cancer Research
> >
> >
>
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