NAME

       alien_hunter  -  Interpolated  Variable  Order  Motifs  for identification of horizontally
       acquired DNA

SYNOPSIS

       alien_hunter <sequence.file> <output.file> [Options]

DESCRIPTION

       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/.

       INPUT: raw genomic sequence PREDICTION: HGT regions based on Interpolated  Variable  Order
       Motifs (IVOMs) arguments:

       <sequence.file>
              raw genomic sequence

       <output.file>
              filename for output data

       Optional arguments:

       -a     to load the prediction file into Artemis

       -c     optimize predicted boundaries with a change-point detection 2 state 2nd order HMM

       Output files:

       <output.file>
              predictions (tab file) in embl format

       <output.file>.opt
              optimized (HMM) predictions (tab file) in embl format

       <output.file>.plot
              predictions  in  Artemis  User Plot format to be loaded manually using Graph -> Add
              User Plot...

       <output.file>.opt.plot
              optimized (HMM) predictions in Artemis User Plot format to be loaded manually using
              Graph -> Add User Plot...

       <output.file>.sco
              the scores over all the sliding windows - for score distribution check

       Note: Predictions that overlap with rRNA operon are mentioned in the note qualifier

SEE ALSO

       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

AUTHOR

       This manual page was written by Andreas Tille <tille@debian.com> for the Debian(TM) system
       (but  may  be  used by others). This man page is released under the same conditions as the
       software, that is GPL.