Bioinformatic and experimental analyses of promoter regions are available for a long time. Finding of the transcription factor binding sites (TFBSs), however, by either method still faces a number of problems. For example, because of the ambiguity of binding of transcription factors, the number of false-positives and -negatives can be unexpectedly high in these sequence analyses. We can assume that evolutionary conserved motifs or regions in the promoters of the homologous genes function as TFBSs. Thus, a comparative genomic approach can provide a partial resolution for the problem previously outlined. This chapter describes application of the DoOP database and the DoOPSearch web tools for such a comparative genomic analysis. Orthologous promoter sequences and conserved motifs can be extracted from the DoOP database for further analysis. The web-based tools of the DoOPSearch webpage can be used for searching and comparing conserved motifs. Using these tools, it is possible to compare short sequences with conserved motifs, to map conserved motifs into a longer promoter region, or find sequence patterns in different sets of promoter sequences.