GenSkew

About 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 (the python library)

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  • Genskew_cc (a commandline client)

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  • GUIskew (the graphical version of GenSkew)

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  • Webskew (the online version)

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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