[Bioperl-l] Pattern Density
osborne1 at optonline.net
Tue Feb 21 21:13:44 UTC 2006
I was mistaken previously when I hinted that you couldn't create histograms
This could do exactly what you want.
On 2/21/06 3:38 PM, "Cook, Malcolm" <MEC at stowers-institute.org> wrote:
> You might consider displaying ccgg content as a track in mouse genome
> browser at
> For example, the following track causes it to display 3 proportionally
> sized red boxes in the first 3K of mouse Chr1
> glyph = xyplot
> graph_type = boxes
> fgcolor = black
> bgcolor = red
> key="Motif Content"
> MotifContent CCGG 1..1000 score=20
> MotifContent CCGG 1001..2000 score=50
> MotifContent CCGG 2001..3000 score=30
> There are many ways for computing the score. I myself would begin with:
> #!/usr/bin/env perl
> use strict;
> use Bio::SeqIO; # for reading sequence to scan
> use TFBS::Word::Consensus; # for the pattern matching. cf.
> use PDL::Basic; # if you have it installed, for the histogram binning
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of staffa
> Sent: Tuesday, February 21, 2006 11:25 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Pattern Density
> Good Friends,
> I have an important client who wants a histogram display of the
> density of "ccgg" along any chromosome of the mouse genome in 1000 bp
> I'm thinking that maybe there is a bio-perl module that could
> help with this.
> That'd probably beat having to write something from scratch.
> Any help that you give would be greatly appreciated.
> I am more concerned about the reading and analysis of the
> sequence than actual plotting of the histogram, but anything you can
> offer will be appreciated.
> Thank you.
> Nick Staffa
> Telephone: 919-316-4569 (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Information Technology Support Services Contract
> (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov )
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina
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