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  identifica-
       tion  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)