[Cdd-commits] r697 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Thu Apr 10 06:08:59 2008
New Revision: 697

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added some information about riso and its relation to smile.  I'm not sure in which statos these both projects are but at least Steffen Möller did some work on smile in the far past.


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Thu Apr 10 06:08:59 2008
@@ -1073,3 +1073,27 @@
  way to obtain the necessary files by using the training procedure of
  GlimmerHMM.
 Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Depends: riso
+Homepage: http://kdbio.inesc-id.pt/~asmc/software/riso.html
+License: not specified
+Pkg-Description: motif discovery tool
+ RISO discovers motifs composed of many binding sites separated by
+ spacers. Each binding site is called a box
+ .
+ The author of SMILE claims at his homepage
+ http://www-igm.univ-mlv.fr/~marsan/smile_english.html that RISO is
+ faster and more powerfull than SMILE which is described itself as
+ "SMILE is a tool that infers motifs in a set of sequences, according
+ to some criterias. It was first made to infer exceptionnal sites as
+ binding sites in DNA sequences. It allows to infer motifs written on
+ any alphabet (even degenerate) in any kind of sequences.  The
+ specificity of SMILE is to allow  to deal with what we call
+ "structured motifs",  which are motifs associated by some distance
+ constraints. In particular, SMILE is able to group under a unique
+ model different occurrences composed of several boxes separated by
+ spacers of different lengths."
+ .
+ The reference to SMILE is made here especially because there is some
+ work done in the Debian Med SVN at
+ http://svn.debian.org/wsvn/debian-med/trunk/packages/smile/trunk/?rev=0&sc=0