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alien_hunter - Online in the Cloud

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This is the command alien_hunter that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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