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隐马尔科夫过程 Profile Hidden Markov Models
Profile Hidden Markov Models Markov models Hidden Markov models Profile hidden Markov models Markov Chain A set of states The transitions from one state to all other states, including itself, are governed by a probability distribution First order Markov chain: the probabilities depend solely on the current state n-th order Markov chain: n previous states A Markov Model of DNA Mutations Two Uses of a Markov Model Generate sequences according to the probabilities Compute the probability of a sequence A Markov Model Generating Random DNA Sequences A Good Introduction to HMM The examples in the following slides are taken from: An introduction to hidden Markov models for biological sequences Anders Krogh In Computational Methods in Molecular Biology, edited by S. L. Salzberg, D.B. Searls, and S. Kasif, pages 45-63, Elsevier, 1998 http://www.binf.ku.dk/users/krogh/publications/ps/Krogh98a.pdf A DNA Motif Regular Expression for the Motif A Problem with Regular Expression A Hidden Markov Model First Three and Last Three Columns Column 1: 4 A’s and 1 T probability for A is 0.8 probability for T is 0.2 Insertions Columns 4, 5, 6 are the insertions At the fourth column, 3 out of 5 sequences have insertions the probability of transition from the third node to the insertion node is 0.6 In the insertion node, 1 A, 2 C’s, 1 G, 1 T the probabilities of A, C, G, T are 0.2, 0.4, 0.2, 0.2 Transitions out of the insertion node 3 out of the 5 insertions terminate the insertion the probability of leaving the insertion node is 0.6 The Probabilities of Sequences A Problem with Probabilities Biased by the lengths of the sequences 0.047 for ACAC--ATC 0.000075 for TCAACTATC Normalize for the length let L be the length of the sequence divide the probability by (0.25)L odds ratio take logarithm of odds ratio: log-odds score Probabilities and Log-odds Scores If There Are No Insertions Remove the insertion node The probabilities of all transitions are 1 log-odds score is 0 Then the score o
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