FYI.
I consider the packaging in our SVN as ready for upload. If
nobody insists I'll do this soon.
Kind regards
Andreas.
----- Forwarded message from Andreas Tille <[email protected]> -----
Subject: Bug#550954: ITP: alien-hunter -- Interpolated Variable Order Motifs to
identify horizontally acquired DNA
From: Andreas Tille <[email protected]>
To: Debian Bug Tracking System <[email protected]>
Date: Wed, 14 Oct 2009 13:59:15 +0200
X-Spam_score: -3.4
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <[email protected]>
* 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/
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