Transcription factors (TFs) regulate gene expression by binding to specific DNA sites in cis regulatory regions of genes. Most eukaryotic TFs are members of protein families that share a common DNA binding domain and often recognize highly similar DNA sequences. Currently, it is not well understood why closely related TFs are able to bind different genomic regions in vivo, despite having the potential to interact with the same DNA sites. Here, we use the Myc/Max/Mad family as a model system to investigate whether interactions with additional proteins (co-factors) can explain why paralogous TFs with highly similar DNA binding preferences interact with different genomic sites in vivo. We use a classification approach to distinguish between targets of c-Myc versus Mad2, using features that reflect the DNA binding specificities of putative co-factors. When applied to c-Myc/Mad2 DNA binding data, our algorithm can distinguish between genomic regions bound uniquely by c-Myc versus Mad2 with 87% accuracy. © 2013 Springer-Verlag.