[Gmod-help] polypeptide view in Gbrowse

[Lincoln Stein]

Oh gee, it looks like I should retire the protein glyph. It definitely isn't
behaving the way I think it should, which is to do the translation itself
based on the phase and dna sequence.

The -draw_protein_target option is *only* supposed to work if you've got a
protein defined as the target which aligns to a dna source -- for example, a
tblastn result.

Lincoln

On Wed, Dec 17, 2008 at 3:12 PM, Newton Vidal <nwvidal at gmail.com> wrote:

> 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
>> >
>> >
>>
>
>


-- 
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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