Fig. 1
From: Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data
Inhomogeneous Parsimonious Markov model of order two for a motif of width 15. The nucleotide distribution of each position in the sequence may depend on the dinucleotide at the two previous positions. Parsimonious context trees (PCTs) are here used for reducing the parameter space by merging context sequences to sets of sequences, interpolating between traditional Markov model (maximal PCT) and the PWM model (minimal PCT). Exemplary PCTs, which cover both special cases and one intermediate case are shown for position 5, position 11, and position 15. The nodes in these PCTs are colored according to the conditioning random variables they correspond to