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University Vienna|CMESS

PhenDB VogDB NVT HoloVir SIMAP EffectiveDB PICA Gepard GenSkew LiSC Upload


 * Gepard
   * Home
   * Webapp
   * Tutorial
 * GenSkew
   * Home
   * Genskew_cc
   * GUIskew
   * Webskew
   * Library Documentation


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.

There are four versions of this Program: Genskew_univiecube (the python
library), Genskew_cc (a commandline client), GUIskew (the graphical version of
GenSkew) and Webskew (the online version).


THE FACES OF GENSKEW

Every version of GenSkew has its own page, where you can find detailed
explaination of usage and other information on them.


GENSKEW_CC

Genskew_cc is the commandline client for GenSkew. It can be installed via pypi
page.

After installing, type

$ python3 -m genskew -h

and you will be presented with a detailed description of how to use it.


GUISKEW

GUIskew is the graphical version of GenSkew. Here you can find how to use it.
For linux and mac it can be installed via the pypi page IF you already have
tkinter installed. On most Linux distros you can install tkinter by the
following command:

$ apt-get install python-tk

For Windows the Programm can also be downloaded here:




WEBSKEW

Webskew is the online version of GenSkew. it functions exactly the same as the
GUIskew program. Here you can find how to use it.


GENSKEW_UNIVIECUBE

Genskew_univiecube is the python library and the backend for all other GenSkew
programs. Here you can find how to use it.. It can be installed via the pypi
page.


THE GRAPH



The Graph you get back from the program should look a bit like the example graph
above. It consists of two lines: the blue skew line and the red cumulative skew
line.

THE SKEW

The blue figure displays the skew over the length of the genome. It is
calculated by seperating the genome into windows. In these windows the two
chosen nucleotides get counted and subjected to the formula:

Skew = (nucleotide1 - nucleotide2) / (nucleotide1 + nucleotide2)

while the x axis is the position in the genome and the y axis the skew.

THE CUMULATIVE SKEW

The ccumulative skew adds up all previous values to a specific position. It also
displays the global minimum and maximum, which are shown in the graph by the two
green lines. These predict the origin of replication (minimum) and the terminus
location (maximum) in prokaryotic genomes.

Furthermore you can change the graph to a SkewIT¹ graph in every version.


REFERENCES

1: SkewIT,
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008439
(06.04.2022), SkewIT: The Skew Index Test for large scale GC Skew analysis of
bacterial genomes, Jennifer Lu, Steven L. Salzberg

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