I'm working on trying to implement a hidden markov model to model the affect of a specific protein that can cut an RNA when the ribosome is translating the RNA slowly.
Some brief background:
The ribosome translates mRNA into protein
The ribosome can occasionally pause on the mRNA due to things such as secondary structure
There is a protein (call it protein $X$) that can cleave the mRNA when the ribosome is paused.
I'd like to build an HMM that can model this process, however It's been difficult to find references. I've seen that some people use absorbing states in continuous time HMM that model disease progression, for example here, however I'd like to do this for a discrete case. Most simply, my HMM would look like:
with the arrows modeling the transitions.
The emissions would be things like secondary structure free energy (a continuous parameter), and which codon is being translated (discrete parameter).
The "cut" state is an absorbing state that cannot be recovered from. Ideally I'd like to be able to run the same sequence through this model and sometimes become "cut" with a certain probability. In the end, I'd like this model to be able to predict whether or not a sequence will be "cut" enough to observe a significant difference between it and a sequence that is less likely to become "cut".
Any help/references would be very much appreciated. Thanks!