[Gmod-help] polypeptide view in Gbrowse
Lincoln Stein
lincoln.stein at gmail.com
Fri Dec 19 13:32:03 EST 2008
Hi,
I have fixed the protein glyph so that it automatically translates DNA into
protein if it is run on top of a dna database. The same restrictions apply
as to the cds glyph -- the phase of the feature's subparts need to be
correctly defined, or you will get nonsense. At high power, the protein
translation appears, just like the cds glyph (I did this by making protein a
subclass of cds).
It is now in CPAN under Bio::Graphics version 1.81.
Lincoln
On Fri, Dec 19, 2008 at 11:57 AM, Scott Cain <cain.cshl at gmail.com> wrote:
> Hi Lincoln,
>
> Before you retire it, consider that people might be using it either
> with GBrowse as a protein viewer (like SGD does, though I don't know
> if they are using the protein glyph) or in some other application that
> uses Bio::Graphics in an application outside of GBrowse for displaying
> protein information. This protein glyph is actually pretty nice in
> that, when zoomed out, it behaves like the dna glyph and displays a kd
> plot, and zoomed in displays the residues.
>
> Scott
>
>
> On Fri, Dec 19, 2008 at 11:45 AM, Lincoln Stein <lincoln.stein at gmail.com>
> wrote:
> > 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>
> >
>
>
>
> --
> ------------------------------------------------------------------------
> 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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