Fig. 6
From: Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data
Sequence logos and position-specific dependency refinements of several transcription factors. We visualize dependencies of order 1–4 for YY1, NANOG, REST, and USF2 by plotting the traditional sequence logo for each TF and show a position-specific refinement by showing the PCT at one position together with the conditional sequence logos of each leaf in the PCT. The width of the conditional sequence logo is scaled according to the number of sequences in the data that match the particular context, with broad nucleotide stacks representing frequent and narrow nucleotide stacks representing infrequent contexts