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. 2010 Aug 4;8(2):92–102. doi: 10.1016/S1672-0229(10)60010-1

Figure 6.

Figure 6

A hidden Markov model (HMM) for nucleosome-DNA interaction. A. Hidden states. Each nucleotide in the sequences has four possibilities to be at the ends of nucleosome-protected sequence: 5′-end (F), 3′-end (T), 5′/3′-end (B), and no-end (N), which correspond to four hidden sates, F, T, B, and N of the HMM. The transitions among four states happen between any two states aside from self transitions. B. Profile HMM. State (S) transition happens only from each nucleotide position (1, 2, 3 … n−2, n−1) to the next nucleotide position (2, 3, 4 … n−1, n) along a DNA sequence. The observation (O) for each state can be any of the four nucleotides. To make use of position-specific information, transition possibilities (t) and emission possibilities (e) are calculated for each nucleotide position independently. C. Abundance of the four HMM states around the 5′-ends of nucleosome-protected sequences. All four states coincide with the 175-nt periodicity in nucleosome data.