Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Software

GPFrontend and GPGraphics: graphical analysis tools for genetic association studies

Steffen Uebe1, Francesca Pasutto1, Mandy Krumbiegel1, Denny Schanze12, Arif B Ekici1 and André Reis1*

Author Affiliations

1 Institute of Human Genetics, University of Erlangen-Nuremberg, Schwabachanlage 10, 91054 Erlangen, Germany

2 Institute of Human Genetics, University of Magdeburg, Leipziger Straße 44, 39120 Magdeburg, Germany

For all author emails, please log on.

BMC Bioinformatics 2010, 11:472  doi:10.1186/1471-2105-11-472

Published: 21 September 2010

Abstract

Background

Most software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems. Graphical output is often not intended or supposed to be performed with other command line tools, e.g. gnuplot.

Results

Using the Microsoft .NET 2.0 platform and Visual Studio 2005, we have created a graphical software package to analyze data from microarray whole genome association studies, both for a DNA-pooling based approach as well as regular single sample data. Part of this package was made to integrate with GenePool 0.8.2, a previously existing software suite for GNU/Linux systems, which we have modified to run in a Microsoft Windows environment. Further modifications cause it to generate some additional data. This enables GenePool to interact with the .NET parts created by us. The programs we developed are GPFrontend, a graphical user interface and frontend to use GenePool and create metadata files for it, and GPGraphics, a program to further analyze and graphically evaluate output of different WGA analysis programs, among them also GenePool.

Conclusions

Our programs enable regular MS Windows users without much experience in bioinformatics to easily visualize whole genome data from a variety of sources.