Abstract
BackgroundMost 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.ResultsUsing 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.ConclusionsOur programs enable regular MS Windows users without much experience in bioinformatics to easily visualize whole genome data from a variety of sources.
Highlights
Most software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems
Originally intended as a graphical extension of an analysis software for pooling based studies, especially GPGraphics has developed into a universal visualization tool for the output of many different analysis programs, such as PLINK or EIGENSTRAT
Since it can be customized to accommodate almost any text output sorted in map order, it enables even inexperienced users to get an overview of whole genome association data and to visually search for loci warranting further study
Summary
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. 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 GenePool
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