[Bioperl-l] Plotting per-nucleotide-score vs. genome

Chris Fields cjfields at illinois.edu
Tue Jun 29 11:18:52 EDT 2010

This is also possible via Bio::Graphics I believe, using some of the xyplot glyphs.  Genome-wide information is probably better described using a compressed format like wig/bigwig (which BioPerl can also read via Lincoln's Bio::BigFile).


On Jun 29, 2010, at 9:51 AM, Peter wrote:

> On Tue, Jun 29, 2010 at 3:01 PM, David Breimann
> <david.breimann at gmail.com> wrote:
>> Hello,
>> I have calculated some numeric score for each nucleotide in some
>> genbank file.I would like to plot these scores against the genome.
> As a quick solution you could use Artemis. Load the GenBank file,
> then menu Graph, Add User Plot, and pick a plot file. There are
> several supported formats but the simplest is one score per line
> (one line per nucleotide). You can use several scores per line (i.e.
> several scores per nucleotide) and then you get several different
> color lines on the plot. See:
> http://www.sanger.ac.uk/resources/software/artemis/
> Peter
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