EnglishFrenchSpanish

OnWorks favicon

alien_hunter - Online in the Cloud

Run alien_hunter in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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

Use alien_hunter online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    PAC Manager
    PAC Manager
    PAC is a Perl/GTK replacement for
    SecureCRT/Putty/etc (linux
    ssh/telnet/... gui)... It provides a GUI
    to configure connections: users,
    passwords, EXPECT regula...
    Download PAC Manager
  • 2
    GeoServer
    GeoServer
    GeoServer is an open-source software
    server written in Java that allows users
    to share and edit geospatial data.
    Designed for interoperability, it
    publishes da...
    Download GeoServer
  • 3
    Firefly III
    Firefly III
    A free and open-source personal finance
    manager. Firefly III features a
    double-entry bookkeeping system. You can
    quickly enter and organize your
    transactions i...
    Download Firefly III
  • 4
    Apache OpenOffice Extensions
    Apache OpenOffice Extensions
    The official catalog of Apache
    OpenOffice extensions. You'll find
    extensions ranging from dictionaries to
    tools to import PDF files and to connect
    with ext...
    Download Apache OpenOffice Extensions
  • 5
    MantisBT
    MantisBT
    Mantis is an easily deployable, web
    based bugtracker to aid product bug
    tracking. It requires PHP, MySQL and a
    web server. Checkout our demo and hosted
    offerin...
    Download MantisBT
  • 6
    LAN Messenger
    LAN Messenger
    LAN Messenger is a p2p chat application
    for intranet communication and does not
    require a server. A variety of handy
    features are supported including
    notificat...
    Download LAN Messenger
  • More »

Linux commands

Ad