[Cdd-commits] r1008 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Fri Jul 25 07:52:55 2008
New Revision: 1008

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added logomat-m


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Fri Jul 25 07:52:55 2008
@@ -1917,3 +1917,24 @@
     'a','c','g','t'. 'n's found in the sequence files will be
     converted to 'c'.
     The output of hexamer is in General Feature Format (GFF) format.
+
+Depends: logomat-m
+Homepage: http://www.sanger.ac.uk/Software/analysis/logomat-m/
+License: As Perl itself
+Pkg-Description: visualize central aspects of Profile Hidden Markov Models (pHMMs)
+ Profile Hidden Markov Models (pHMMs) are a widely used tool for
+ protein family research. We present a method to visualize all of
+ their central aspects graphically, thus generalizing the concept of
+ sequence logos introduced by Schneider and Stephens. For each
+ emitting state of the pHMM, we display a stack of letters. As for
+ sequence logos, the stack height is determined by the deviation of
+ the position's letter emission frequencies from the background
+ frequencies of the letters. As a new feature, the stack width now
+ visualizes both the probability of reaching the state (the hitting
+ probability) and the expected number of letters the state emits
+ during a pass through the model (the expected contribution).
+ .
+ If you use HMM-Logos in your publication, please cite HMM Logos for
+ visualization of protein families.  Schuster-Böckler B, Schultz J,
+ Rahmann S BMC Bioinformatics. 2004;5;7. PMID: 14736340 DOI:
+ 10.1186/1471-2105-5-7