A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs
(A) Motif network of nuclear receptor motifs with colors indicating clusters extracted by MCL. (B) Phylogeny of nuclear receptor DNA-binding domains represented by matrices in the motif network. Branch colors correspond to MCL clusters in A. (C) Motif logos were generated using WebLogo  for binding sites of NR3C proteins (top), estrogen receptor (middle), and nuclear receptors from other families (bottom). The half-site logos illustrate that estrogen receptor motifs were correctly clustered separately from NR3C matrices and with the other nuclear receptors.