Computational Biology Scribe Notes for Class 15
June 12, 2000

Scribe: J. Zwolak

Markov Models -- A model in statistics where the only requirement to find the probability of the next state is the current state. Some interesting properties are: reachability and irreducibility. Reachability is when you can get to state i from state j through some transitions. Irreducibility is when you can get to any state from any other state through some transitions.
Hidden Markov Models (HMM) -- They can be used to model alignment. That is where we left off in class.
Regular Languages -- Regular languages are expressed in regular expressions, deterministic finite state machines, and non-deterministic finite state machines. These may be used to search for genes in a long sequence of DNA.
Mealy and Moore Machines -- These two machine models have there own way of adding output to the deterministic finite state machine. The Mealy machine has output associated with the transition. The Moore machine has output associated with the state. The output of these machines may be useful in scoring a sequence.

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