Bug#550954: ITP: alien-hunter -- Interpolated Variable Order Motifs to identify horizontally acquired DNA

[Andreas Tille <tillea@rki.de>]

Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tillea@rki.de>

* Package name    : alien-hunter
  Version         : 1.7
  Upstream Author : George Vernikos
* URL             : http://www.sanger.ac.uk/Software/analysis/alien_hunter/
* License         : GPL
  Programming Lang: Perl, Java
  Description     : Interpolated Variable Order Motifs to identify 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

I intend to maintain this package in the Debian Med Packaging Team.
Packaging stuff is just commited to

  Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/alien-hunter/trunk/