[Bioperl-l] CG content plot of sequence

[Chris Fields]

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
>
> -- 
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>
> -- 
> ------------------------------------------------
> 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
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign