Skip to main content
. Author manuscript; available in PMC: 2012 Jul 29.
Published in final edited form as: J Stat Phys. 2011 Apr;142(6):1187–1205. doi: 10.1007/s10955-010-0102-x

Fig. 1.

Fig. 1

Hidden Markov Model for binding sites of size l. (Top) There are l + 1 hidden states, with state 0 background DNA and state j corresponding to position j = 1 . . . l in a binding site. The HMM is described by a Markov process with transition probabilities give by aij . (Middle) Each state j in an HMM is characterized by an observation symbol probability bj (k), for the probability of seeing symbol k = A, T , C, G in a state j. (Bottom) A given sequence of DNA is composed of binding sites and background DNA