EnglishFrenchSpanish

Ad


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
    AstrOrzPlayer
    AstrOrzPlayer
    AstrOrz Player is a free media player
    software, part based on WMP and VLC. The
    player is in a minimalist style, with
    more than ten theme colors, and can also
    b...
    Download AstrOrzPlayer
  • 2
    movistartv
    movistartv
    Kodi Movistar+ TV es un ADDON para XBMC/
    Kodi que permite disponer de un
    decodificador de los servicios IPTV de
    Movistar integrado en uno de los
    mediacenters ma...
    Download movistartv
  • 3
    Code::Blocks
    Code::Blocks
    Code::Blocks is a free, open-source,
    cross-platform C, C++ and Fortran IDE
    built to meet the most demanding needs
    of its users. It is designed to be very
    extens...
    Download Code::Blocks
  • 4
    Amidst
    Amidst
    Amidst or Advanced Minecraft Interface
    and Data/Structure Tracking is a tool to
    display an overview of a Minecraft
    world, without actually creating it. It
    can ...
    Download Amidst
  • 5
    MSYS2
    MSYS2
    MSYS2 is a collection of tools and
    libraries providing you with an
    easy-to-use environment for building,
    installing and running native Windows
    software. It con...
    Download MSYS2
  • 6
    libjpeg-turbo
    libjpeg-turbo
    libjpeg-turbo is a JPEG image codec
    that uses SIMD instructions (MMX, SSE2,
    NEON, AltiVec) to accelerate baseline
    JPEG compression and decompression on
    x86, x8...
    Download libjpeg-turbo
  • More »

Linux commands

  • 1
    abi-tracker
    abi-tracker
    abi-tracker - visualize ABI changes
    timeline of a C/C++ software library.
    DESCRIPTION: NAME: ABI Tracker
    (abi-tracker) Visualize ABI changes
    timeline of a C/C+...
    Run abi-tracker
  • 2
    abicheck
    abicheck
    abicheck - check application binaries
    for calls to private or evolving symbols
    in libraries and for static linking of
    some system libraries. ...
    Run abicheck
  • 3
    couriermlm
    couriermlm
    couriermlm - The Courier mailing list
    manager ...
    Run couriermlm
  • 4
    couriertcpd
    couriertcpd
    couriertcpd - the Courier mail server
    TCP server daemon ...
    Run couriertcpd
  • 5
    gbklatex
    gbklatex
    bg5latex - Use LaTeX directly on a Big5
    encodedtex file bg5pdflatex - Use
    pdfLaTeX directly on a Big5 encodedtex
    file bg5+latex - Use LaTeX directly on a
    Big5+...
    Run gbklatex
  • 6
    gbkpdflatex
    gbkpdflatex
    bg5latex - Use LaTeX directly on a Big5
    encodedtex file bg5pdflatex - Use
    pdfLaTeX directly on a Big5 encodedtex
    file bg5+latex - Use LaTeX directly on a
    Big5+...
    Run gbkpdflatex
  • More »

Ad