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.