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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.