References

• Hidden Markov models were originally invented and are commonly used for speech recognition. For additional material on this subject, see [9].
• For a more comprehensive overview on the EM technique, see [1].

• For a detailed discussion about the adaptation of HMMs to computational biology algorithms see [4] (chapters 3-6).

• Applications of profile HMMs for multiple alignment of proteins can be found in [5] and for finding genes in the DNA can be found in [7,6].