Alien_hunter

Overview

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.

License

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.

Reference

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 and Parkhill J

  Bioinformatics (Oxford, England) 2006;22;18;2196-203

  PUBMED: 16837528; DOI: 10.1093/bioinformatics/btl369

Contact

For questions or comments, please contact dna-hunt@sanger.ac.uk.

Downloads

FTP download

The latest release of Alien_hunter available for Unix is available for download via FTP:

• Alien_hunter for UNIX

Source code

The alien_hunter source code is also available from the Sanger Institute web CVS server in the alien_hunter repository. To checkout the code from the repository by logging in with:

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:cvsuser@cvs.sanger.ac.uk:/cvsroot/pathsoft co alien_hunter

(If downloaded from CVS you should compile the two java files first).

Alien_hunter needs a recent version of PERL v5.6.1 and JAVA SDK v1.4.2. or higher.

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:

./alien_hunter

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

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.