[Cdd-commits] r994 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Tue Jul 22 09:48:46 2008
New Revision: 994

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


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Tue Jul 22 09:48:46 2008
@@ -1685,3 +1685,25 @@
  to know what the people are doing with the sources (compile the
  sources on a new architectures,  modify the code for their own
  research project, etc.)
+
+Depends: alien_hunter
+Homepage: http://www.sanger.ac.uk/Software/analysis/alien_hunter/
+License: GPL
+Pkg-Description: Interpolated Variable Order Motifs for identification of horizontally acquired DNA
+ alien_hunter is an application for the prediction of putative Horizontal
+ Gene Transfer (HGT) events with the implementation of Interpolated Variable
+ Order Motifs (IVOMs). An IVOM approach exploits compositional biases using
+ variable order motif distributions and captures more reliably the local
+ composition of a sequence compared to fixed-order methods. Optionally the
+ predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM),
+ in a change-point detection framework, to optimize the localization of the
+ boundaries of the predicted regions. The predictions (embl format) can be
+ automatically loaded into Artemis genome viewer freely available at:
+ http://www.sanger.ac.uk/Software/Artemis/.
+ .
+ The manuscript describing the alien_hunter algorithm is available from
+ Bioinformatics: Interpolated variable order motifs for identification of
+ horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.
+ Vernikos GS, Parkhill J Bioinformatics. 2006;. PMID: 16837528
+Comment: The archive contains biojava 1.4 - but we should focus on
+ Debian packaged BioJava.