THANK YOU FOR HELPING ME CpG islands or CG islands are genomic regions that cont
ID: 63794 • Letter: T
Question
THANK YOU FOR HELPING ME CpG islands or CG islands are genomic regions that contain a high frequency of C and G nucleotides. They are often found in gene promoters and are important for regulation of gene expression.
QUESTION: In HMM models, the transition probabilities leaving a particular hidden state should always add up to 1 (i.e. the probabilities of the arrows going out from a state should add up to 1). Is this the same for the probabilities entering a particular state? In other words, do the probabilities of the arrows pointing towards a state add always add up to 1? Can you explain this?
Explanation / Answer
The symbol l denotes the rate parameter of the transition from State 0 to State 1.
In hidden state HMM there is need to represent both transition and hidden probabilities. In hidden model it is not necessary .
All sequences have to start in state 0 (the begin state), so the initial condition is that v0(0) = 1. By keeping pointers backwards, the actual state sequence can be found by backtracking.To simulate in one model the ‘islands’ in a ‘sea’ of non-island genomic sequence, we want to have both the Markov chains of the last section present in the same model, with a small probability of switching from one chain to the other at each transition point. this introduces the complication that we now have two states corresponding to each nucleotide symbol.
The transition probabilities in this model are set so that within each group they are close to the transition probabilities of the original component model, but there is also a small but finite chance of switching into the other component. Overall there is more chance of switching from ‘+’ to ‘’ than vice versa, so if left to run free, the model will spend more of its time in the ‘’ non-island states than in the island states
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