ppt课件-markovmodels-utahstateuniversity.pptVIP

Markov Models Charles Yan 2008 Markov Chains A Markov process is a stochastic process (random process) in which the probability distribution of the current state is conditionally independent of the path of past states, a characteristic called the Markov property. Markov chain is a discrete-time stochastic process with the Markov property I will use a gene finding example (to be exactly, CpG islands identification) to show Markov chains, since it is a simple and well-studied case. The same approach can be used to other problems. Markov Chains The CG island is a short stretch of DNA in which the frequency of the CG sequence is higher than other regions.? It is also called the CpG island, where p simply indicates that C and G are connected by a phosphodiester bond. Whenever the dinucleotide CpG occurs, the C nucleotide is typically chemically modified by methylation. C of CpG is methylated into methyl-C. methyl-C mutates into T relatively easily. Markov Chains Thus, in general, CpG dinuclueotides are rarer in the genome. F (CpG) f(C) * f(G). Methylation process is supressed before the “starting point” of many genes. These regions (CpG islands) have more CpG than elsewhere. Usually, CpG islands are a few hundred to a few thousand bases long. Identification of CpG islands is important for gene finding. Markov Chains Markov Chains We want to develop a probabilistic model for CpG islands, such that every CpG island sequence is generated by the model. Since dinucleotides are important, we want a model that generates sequences in which the probability of a symbol depends on the previous symbol. The simplest one is a Markov chain. Markov Chains Markov Chains Training the model, i.e., estimate the transition probabilities Prediction Using Data-Mining Approach Markov Chains The probability that a sequence x is generated by a Markov chain model By applying many times of Markov Chains One assumption of Markov chain is that the