alien_hunter

ALIEN_HUNTER(1)                  User Commands                 ALIEN_HUNTER(1)



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.



alien_hunter 1.7                 October 2009                  ALIEN_HUNTER(1)