SYNOPSISalien_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:
- raw genomic sequence
filename for output data
- to load the prediction file into Artemis
optimize predicted boundaries with a change-point detection 2 state 2nd order HMM
- predictions (tab file) in embl format
- optimized (HMM) predictions (tab file) in embl format
- predictions in Artemis User Plot format to be loaded manually using Graph -> Add User Plot...
- optimized (HMM) predictions in Artemis User Plot format to be loaded manually using Graph -> Add User Plot...
the scores over all the sliding windows - for score distribution check
Note: Predictions that overlap with rRNA operon are mentioned in the note qualifier
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.