An introduction to hidden Markov models.

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.

[1]  L. Baum,et al.  Statistical Inference for Probabilistic Functions of Finite State Markov Chains , 1966 .

[2]  L. Baum,et al.  A Maximization Technique Occurring in the Statistical Analysis of Probabilistic Functions of Markov Chains , 1970 .

[3]  E. Neuburg.  Markov Models for Phonetic Text , 1971 .

[4]  J. Baker,et al.  The DRAGON system--An overview , 1975 .

[5]  Frederick Jelinek,et al.  Speech Recognition by Statistical Methods , 1976 .

[6]  James A. Reeds,et al.  On the cryptanalysis of rotor machines and substitution - permutation networks , 1982, IEEE Trans. Inf. Theory.

[7]  L. R. Rabiner,et al.  On the application of vector quantization and hidden Markov models to speaker-independent, isolated word recognition , 1983, The Bell System Technical Journal.

[8]  Hermann Ney,et al.  Connected digit recognition using vector quantization , 1984, ICASSP.

[9]  Lawrence R. Rabiner,et al.  A tutorial on hidden Markov models and selected applications in speech recognition , 1989, Proc. IEEE.

[10]  M. A. McClure,et al.  Hidden Markov models of biological primary sequence information. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[11]  S. Eddy.  Hidden Markov models. , 1996, Current opinion in structural biology.

[12]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[13]  M. Borodovsky,et al.  GeneMark.hmm: new solutions for gene finding. , 1998, Nucleic acids research.

[14]  Jörg Schultz,et al.  HMM Logos for visualization of protein families , 2004, BMC Bioinformatics.

[15]  R. Durbin,et al.  GeneWise and Genomewise. , 2004, Genome research.

[16]  Irmtraud M. Meyer,et al.  Gene structure conservation aids similarity based gene prediction. , 2004, Nucleic acids research.

[17]  Sean R Eddy,et al.  What is a hidden Markov model? , 2004, Nature Biotechnology.

[18]  Johannes Söding,et al.  Protein homology detection by HMM?CHMM comparison , 2005, Bioinform..

[19]  Alex Bateman,et al.  Visualizing profile-profile alignment: pairwise HMM logos , 2005, Bioinform..

[20]  M. S. Ryan,et al.  The Viterbi Algorithm 1 1 The Viterbi Algorithm . , 2009 .