For sets of S.cerevisiae promoters, we used 1200 results from 400 BioProspector runs in our evaluation. For GABRps, we considered all 127 non-empty subsets of the seven promoters (orthologous sequences were always considered together). We used results from 70 000 BioProspector runs, evenly distributed across all promoter subsets, in our analysis. In addition to dust filtering, we required putative TFBSs to occur both in the human and in the orthologous rodent promoter.