[Bioperl-l] CG content plot of sequence

Chris Fields cjfields at uiuc.edu
Wed Oct 3 15:10:46 EDT 2007

On Oct 3, 2007, at 1:31 PM, Vesselin Baev wrote:

> 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!

It would be GC content, not CpG.  Not sure what you would use for  
dinucleotide content; you could look at the Bio::Graphics::Glyph::dna  
code and either subclass it for your needs (probably the best option)  
or add an extra parameter and 'rewire' the appropriate methods to do  
what you want.


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