[Blends-commit] r3361 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Fri May 25 11:58:53 2012
New Revision: 3361

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3361
Log:
logomat-m data now in VCS

Modified:
    projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=3361&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Fri May 25 11:58:53 2012
@@ -350,6 +350,8 @@
 Depends: dazzle
 
 Depends: forester
+
+Depends: logomat-m
 
 Depends: molekel
 
@@ -1581,27 +1583,6 @@
     '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-B"ockler B, Schultz J,
- Rahmann S BMC Bioinformatics. 2004;5;7. PMID: 14736340 DOI:
- 10.1186/1471-2105-5-7
 
 Depends: coot
 Homepage: http://www.ysbl.york.ac.uk/~emsley/coot/