This cumulative dissertation is wridden in english and includes six papers from the bioinformatics area. The aim of these papers is an unterstanding of biological processes on the systems biology level. For this purpose I published different open-source, freely available software tools.The six publications are rooted in the three bioinformatics fields (i) “Phylogenetic footprinting”, (ii) “Data Processing and Interpretation of Mass Spectrometry Data”, and (iii) the “Integration of biological data”. In field (i) the precise prediction and objective comparison of transcription factor binding motifs is covered. In field (ii) the extraction of metabolite signals from mass spectrometry data and the analysis of these on the level of metabolite families is covered. In field (iii) the software tools VANTED is developed further.