CUBE

GenSkew

GenSkew is an application for computing and plotting nucleotide skew data.

GenSkew calculates the incremental and the cumulative skew of two selectable nucleotides for a given sequence according to this formula: Skew = (nucleotide1 - nucleotide2) / (nucleotide1 + nucleotide2)

The results are provided as data table and as graphical plot. The global minimum and maximum are displayed in the cumulative graph. The minimum and maximum of a GC-skew can be used to predict the origin of replication (minimum) and the terminus location (maximum) in prokaryotic genomes.

We provide four versions of this program:

  • Genskew_univiecube

    Genskew_univiecube is the python library of GenSkew and the backend of all other GenSkew applications.

    Installation: pip install Genskew-univiecube

    Documentation: https://pypi.org/project/Genskew-univiecube

  • Genskew_cc

    Genskew_cc is the commandline client for GenSkew.

    Installation: pip install Genskew-cc

    Documentation: https://pypi.org/project/Genskew-cc

  • GUIskew

    GUIskew is the graphical version of GenSkew.

    Prerequisites: tkinter or python-tk (depending on OS and distribution)

    Installation: pip install GUIkew

    Documentation: https://pypi.org/project/GUIskew

  • Webskew

    The GenSkew application is available on the LiSC galaxy server.

    How to use GenSkew online:

    1. Navigate to the LiSC galaxy server
    2. Upload your nucleotide fasta file
    3. Open the "CUBE tools" section
    4. Configure and run GenSkew