One of the limiting factors in deciphering transcriptional regulatory networks is the effectiveness of motif-finding software. An emerging avenue for improving motif-finding accuracy aims to incorporate generalized binding constraints of related transcription factors (TFs), named familial binding profiles (FBPs), as priors in motif identification methods. A motif-finder can thus be biased towards finding motifs from a particular TF family. However, current motif-finders allow only a single FBP to be used as a prior in a given motif-finding run. In addition, current FBP construction methods are based on manual clustering of position specific scoring matrices (PSSMs) according to the known structural properties of the TF proteins. Manual clustering assumes that the binding preferences of structurally similar TFs will also be similar. This assumption is not true, at least not for some TF families. Automatic PSSM clustering methods are thus required for augmenting the usefulness of FBPs.