[Bioperl-l] CG content plot of sequence

[Vesselin Baev]

Thanks,
I will use Bio::Graphics::Glyph::dna for the classical CG%
(this type is for C+G % or CpG)?


and if I want to draw a similar plot but for example for a % of dinucleotide
(NpN) occurrances in a sliding windiw, what should I use?


Thanks!




2007/10/3, Chris Fields <cjfields at uiuc.edu>:
>
> You should look at Bio::Graphics::Glyph::dna.  From the POD:
>
> ---------------------------
>
> This glyph draws DNA sequences.  At high magnifications, this glyph
> will draw the actual base pairs of the sequence (both strands).  At
> low magnifications, the glyph will plot the GC content.  By default,
> the GC calculation will use non-overlapping bins, but this can be
> changed by specifying the gc_window option, in which case, a
> sliding window calculation will be used.
>
> For this glyph to work, the feature must return a DNA sequence string
> in response to the dna() method. For example, you can use a
> Bio::SeqFeature::Generic object with an attached Bio::PrimarySeq
> like this:
>      my $dna = Bio::PrimarySeq->new( -seq => 'A' x 1000 );
>      my $feature = Bio::SeqFeature::Generic->new( -start => 1, -end
> => 800 );
>      $feature->attach_seq($dna);
>      $panel->add_track( $feature, -glyph => 'dna' );
>
> A Bio::Graphics::Feature object may also be used.
>
> ---------------------------
>
> chris
>
> On Oct 3, 2007, at 11:44 AM, Vesselin Baev wrote:
>
> > Hi,
> > What methods should I use to draw a CG plot of a sequence (with
> > bio::graphics)?
> >
> > Thanks
> >
> > --
> > ------------------------------------------------
> > University of Plovdiv
> > Faculty of Biology
> > Dept. Molecular Biology
> > Bioinformatics Group
> > Tzar Assen 24
> > Plovdiv 4000, BULGARIA
> > 032/ 261 (534)
> > 089/ 57-444-67
> > Skype: vesselin_baev
> > vebaev at gmail.com
> >
> > --
> > ------------------------------------------------
> > University of Plovdiv
> > Faculty of Biology
> > Dept. Molecular Biology
> > Bioinformatics Group
> > Tzar Assen 24
> > Plovdiv 4000, BULGARIA
> > 032/ 261 (534)
> > 089/ 57-444-67
> > Skype: vesselin_baev
> > vebaev at gmail.com
> > _______________________________________________
> > Bioperl-l mailing list
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>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>


-- 
------------------------------------------------
University of Plovdiv
Faculty of Biology
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 57-444-67
Skype: vesselin_baev
vebaev at gmail.com