Interpolated variable order motifs for identification of horizontally acquired dna
alien_hunter <sequence.file> <output.file> [Options]
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
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
This manual page was written by Andreas Tille <[email protected]> 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.