Comparison of predicted and phage display determined binding specificities. A comparison of phage display determined and predicted PDZ domain binding specificities for the last five terminal binding positions visualized as sequence logos. The binding specificity similarity between two domains was computed using the normalized Euclidean distance between their corresponding position weight matrices (see Additional file 1, equation 1). Non-genomic phage display peptides were removed from the set of binders for each domain. Only domains with four or more peptides after this filter were used to create sequence logos describing the domain’s binding specificity. Based on a previously established protocol, a peptide was considered to be genomic if the last four residues could be found in a proteomic tail, otherwise it was considered to be non genomic. Numbers in bold indicate which similarity (sequence or structure) is higher (i.e. which predicted logo is closer to the experimental logo).