[Bioperl-l] Pattern Density

Brian Osborne osborne1 at optonline.net
Tue Feb 21 16:13:44 EST 2006


Nick,

I was mistaken previously when I hinted that you couldn't create histograms
using Bioperl:

http://doc.bioperl.org/releases/bioperl-1.5.0-RC1/Bio/Graphics/Glyph/xyplot.
html

This could do exactly what you want.

Brian O.


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
> http://gbrowse.informatics.jax.org/cgi-bin/gbrowse/mouse_build_34
>  
> For example, the following track causes it to display 3 proportionally
> sized red boxes in the first 3K of mouse Chr1
> 
> [MotifContent]
> glyph = xyplot
> graph_type = boxes
> fgcolor = black
> bgcolor = red
> height=100
> min_score=0
> max_score=100
> label=1
> key="Motif Content"
> 
> reference=Chr1
> 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.
> http://forkhead.cgb.ki.se/TFBS/
> use PDL::Basic; # if you have it installed, for the histogram binning
> statistics 
> 
>  
>  
> 
> 
> 
> ________________________________
> 
> 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
> windows. 
> 
> 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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