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This unit introduces the concept of hidden Markov models in computational biology. It describes them using simple biological examples, requiring as little mathematical knowledge as possible. The unit also presents a brief history of hidden Markov models and an overview of their current applications before concluding with a discussion of their limitations.

Original publication




Journal article


Curr Protoc Bioinformatics

Publication Date



Appendix 3


Appendix - 3A


Algorithms, Artificial Intelligence, Computer Simulation, Data Interpretation, Statistical, Markov Chains, Models, Biological, Models, Statistical, Pattern Recognition, Automated, Sequence Analysis