[Bioperl-l] Pattern Density
MEC at stowers-institute.org
Tue Feb 21 20:38:55 UTC 2006
You might consider displaying ccgg content as a track in mouse genome
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
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:
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
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.
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