[Bioperl-l] Pattern Density

[Cook, Malcolm]

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