Figure 1

The idea behind the Regulatory Modules kernel: A motif finder is applied to regulatory sequences (long, gray bars) and identifies overrepresented motifs (colored segments). Around the best-matching motifs (boxed) in every sequence we excise 20 base pairs around the center. Conservation information and the pairwise distances of motifs to each other and to the end of the sequence are added to form the Regulatory Modules kernel, concatenating feature spaces.