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DNA-chip experiments result in fluorescence images showing complex hybridization spot patterns which are tedious to interpret by eye. The first step in its analysis is applying a software for microarray image analysis. Fluorescence and background signals are quantified on each spot and stored in a numerical list. This is, however, just a small step towards the result suitable for a biologist.
In the second step this list of fluorescence signals has to be interpreted regarding parameters set by the researcher and, thereby, translated into results suitable and meaningful for biologists (e.g. a list of identified organisms or genes). With large numbers of probes on the chip a manual performance of the second step becomes difficult and tedious.
Now, this procedure will be performed automatically by our simple command line oriented software "ChipChecker". It has been developed within the project "Development of Oligonucleotide DNA-Chips - Universal DNA-Chip for the Detection of Microorganisms", granted by the Bayerische Forschungsstiftung, in cooperation with the Department for Microbiology of the TU München.
The first application of ChipChecker was the interpretation of data retrieved from studies with a newly developed DNA-chip for the identification of sulfate reducing microorganisms in complex samples. A manuscript about this work has recently been submitted to Applied and Environmental Microbiology (An Oligonucleotide Microarray for 16S rRNA Gene-based Detection of all Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment by Alexander Loy, Angelika Lehner, Natuschka Lee, Justyna Adamczyk, Harald Meier, Jens Ernst, Karl-Heinz Schleifer, and Michael Wagner).
Feel free to download "ChipChecker" from this side for analyzing your results of DNA-Chip studies. You can either fetch and run the binary of ChipChecker (gcc on Linux 7.3) or fetch the ChipChecker-Source and compile it on your system (e.g. gcc -o chipchecker chipchecker.c. Please read the usage description for "ChipChecker" carefully, especially keep an eye on the description of the input files format and on the examples given.
The usage of ChipChecker, the meaning of parameters and options, and the format of input data are described in "README ChipChecker".
You can test ChipChecker with original data from microarray experiments described in the manuscript mentioned above. For this aim, please download the "Testfiles for ChipChecker". Further information about these files you will find in "README ChipChecker"!
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Last modified: Fri Feb 13 13:31:39 CEST 2009 by
