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 the freely available Artemis genome viewer.
Download and Installation
The latest release of Alien_hunter available for Unix is available for download via FTP:
cvs -d :pserver:cvsuser(cvs.sanger.ac.uk:/cvsroot/pathsoft login cvsuser
using CVSUSER as the password.
Then checkout alien_hunter with:
cvs -d :pserver:email@example.com:/cvsroot/pathsoft co alien_hunter
(If downloaded from CVS you should compile the two java files first).
After downloading alien_hunter.tar.gz, change directory to the directory you wish to install alien_hunter in. Extract the alien_hunter.tar.gz file. On UNIX the command is:
gzip -d < alien_hunter.tar.gz | tar xf
This will create a directory called /alien_hunter which will contain all the files necessary for running alien_hunter. If JAVA and PERL is correctly setup on your system, (while in the alien_hunter directory) type:
on the command line to get the main page of alien_hunter.
You will need to setup Artemis executable (art) correctly on your system to use the "-a" option of alien_hunter.
License and Citation
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
For questions or comments, please contact firstname.lastname@example.org.
Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.
Bioinformatics (Oxford, England) 2006;22;18;2196-203