Exploration methods to investigate the evolution of transcriptional regulation in the eukaryotic genome Bioinformatik Genregulation Genetic Evolution Evolution der Genregulation Transkriptionsfaktorbindestellen Transcription Factor Binding Site Bioinformatics Position Specific Scoring Matrix Background: Computational tools for the investigation of transcriptional regulation in particular of transcription factor binding sites (TFBS) in evolutionary context are developed. Existing sequence based tools prediction such binding sites do not consider their actual functionality although it is known that besides the base sequence many other aspects are relevant for binding and for the effects of that binding. In particular in Eukaryotes a perfectly matching sequence motif is neither necessary nor sufficient for a functional transcription factor binding site. Published work in the field of transcriptional regulation frequently focus on the prediction of putative transcription factor binding sites based on sequence similarity to known binding sites. Furthermore among the related software only a small number implements visualization of the evolution of transcription factor binding sites or the integration of other regulation related data. The interface of many tools is made for computer scientists although the actual interpretation of their outcome needs profound biological background knowledge. Results and Discussion: The tool presented in this thesis ReXSpecies is a web application. Therefore it is ready to use for the end user without installation providing a graphical user interface. Besides extensive automation of analyses of transcriptional regulation (the only necessary input are the genomic coordinates of a regulatory region) new techniques to visualize the evolution of transcription factor binding sites were developed ...