Genskew

GenSkew: Genomic nucleotide skew application

Overview

GenSkew is an application for computing and plotting nucleotide skew data. It was developed at the TU Munich, Genome oriented bioinformatics during a 2 weeks-practical in bioinformatics programming by the students Miroslava Edelstein, Florian Gehrke, Sonja Hopf, Andre Jehl and Annahita Oswald, supervised by Thomas Rattei.
Since 2010, GenSkew is maintained by the Department of Computational Systems Biology of the University of Vienna.

The software is based on Java 2, using swing classes. The online application was realized as Java Servlet running on a Tomcat server.

Introduction

The software GenSkew computes the normal and the cumulative skew of two selectable nucleotides for a given sequence. The result is displayed in two different graphs. The user can choose the pair of nucleotides the skew should be calculated for. In such a skew the relation of the nucleotides is given by a formula. The particular values are computed by the formula:

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

For the computation the genome is separated into parts, socalled windows. For every window the value of the skew is calculated with the formula. The normal graph displays every single value related to the particular position in sequence. The cumulative graph adds up the values for all previous windows up to the certain position. The windows are shifted along the sequence by a certain stepsize. To improve the result the stepsize can be reduced.

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.

Availibility

GenSkew is available free of charge and can be used both online and offline:

Tutorial for the GenSkew Java Application

How to access a file

After starting the program you can open a file by using the menue (File/open). Please notice that only text files containing a single sequence without any additions or the sequence in FASTA-format are allowed.

After loading the file the program automatically draws the graphic using the default settings (nucleotides G and C, resolution 1024x768, windowsize and stepsize sequencelength/1000).

How to change settings

The windowsize, the stepsize and the nucleotides are selectable. It is not allowed to select the same nucleotide in both fields (e.g. A and A). If this happens the complementair nucleotide is automatically set for the second field.

If you increase the windowsize and decrease the stepsize you will get more significant values but the calculating time will be longer depending on the capacity of the computer you use. That's why the step- and windowsize are limited.

Negative values are not allowed. Therefore the value will be set one by default if you try to type negative ones. The sizes for the window and the step are restricted as well. For large genomes the size for the window must be smaller than the length of sequence divided by 10000 and the stepsize must be larger then the length of the sequence divided by 1000. If you change the settings the skew will be automatically recomputed.

How to save the results

You can save the results in different forms. The graphic can be saved in jpg- or png-format (File/save plot as image). The first column in the text file lists the positions of the single values, the second column shows the normal and the third column the cumulative values. The data of the skew can be saved as a text file (File/Save plot as text). You can use this file to export the data into a spreadsheet program (e.g. Excel) to create a diagram with your own settings.

The program types the minimum of the cumulative graph of the computed skew into the field "oriC".

You can also save the sequence with the calculated origin of replication as start point of the sequence. You can decide to change the value of the origin. After changing the origin this field is protected and marked yellow even if a new plot is computed. If you want to save the rearranged sequence press File/Save sequence.

System requirements:

Java2 (1.4.2 or newer)

Operating Systems: Every OS that runs Java2 (tested on Linux, Windows, MacOS X)

Contact

For questions, feedback and bug reports please contact Thomas Rattei.