Flow diagram of PePPER all-in-one. The first step of PePPER all-in-one is to select a set of genes that putatively belong to a certain regulon in one organism (target; Box I represents all genes of the target organism) through comparison with the corresponding regulons in all other organisms (source) using protein Blast (genes in Box Ia). In parallel, the known TFBSs of these regulons are used to find genes in the target organism that carry this DNA motif in their upstream regions (genes in Box Ib). Subsequently, a MEME search is performed on the upstream regions of the genes in both independently obtained gene pools. This results in a set of genes that represents the putative regulon in the target organism with its predicted TFBS (genes in Box II). Finally, features such as RBSs, promoter and transcription terminators are added, after which the result is graphically represented. The information can be accessed and viewed separately per gene.