An Introduction to Hidden Markov Models

Benjamin Schuster‐Böckler1, Alex Bateman1

1 Wellcome Trust Sanger Institute, Hinxton, Cambridge
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Appendix 3A
DOI:  10.1002/0471250953.bia03as18
Online Posting Date:  June, 2007
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Abstract

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.

Keywords: Markov Chains; HMM; hidden Markov Models; Machine Learning; Sequence Analysis

     
 
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Table of Contents

  • History
  • Common Applications
  • Markov Models
  • Hidden Markov Models
  • Profile Methods for Sequence Analysis
  • Pair HMMs
  • Drawbacks
  • Conclusions
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
   Baldi, P., Chauvin, Y., Hunkapiller, T., and McClure, M.A. 1994. Hidden Markov models of biological primary sequence information. PNAS 91:1059‐1063.
   Baum, L.E. and Petrie, T. 1966. Statistical inference for probabilistic functions of finite state Markov chains. Ann. Math. Stat. 37:1554‐1563.
   Birney, E., Clamp, M., and Durbin, R., 2004. GeneWise and Genomewise. Genome Res. 14:988‐995.
   Burge, C. and Karlin, S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268:78‐94.
   Durbin, R., Eddy, S.R., Krogh, A., and Mitchison, G. 1998. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, U.K.
   Eddy, S.R. 1996. Hidden Markov models. Curr. Opin. Struct. Biol. 6:361‐365.
   Eddy, S.R. 2004. What is a hidden Markov model? Nat. Biotechnol. 22:1315‐1316.
   Kulp, D., Haussler, D., Reese, M.G., and Eeckman, F.H. 1996. A generalized hidden Markov model for the recognition of human genes in DNA. Proc. Int. Conf. Intell. Syst. Mol. Biol. 4:134‐142.
   Lukashin, A.V. and Borodovsky, M. 1998. GeneMark.hmm: New solutions for gene finding. Nucl. Acids Res. 26:1107‐1115.
   Madera, M. 2005. Hidden Markov models for detection of remote homology. PhD thesis, University of Cambridge, MRC Laboratory of Molecular Biology, May 2005.
   Meyer, I.M. and Durbin, R. 2004. Gene structure conservation aids similarity based gene prediction. Nucl. Acids Res. 32:776‐783.
   Rabiner, L.R. 1989. A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77:257‐286.
   Schuster‐Böckler, B. and Bateman, A. 2005. Visualizing profile‐profile alignment: Pairwise HMM logos. Bioinformatics 21:2912‐2913.
   Schuster‐Böckler, B., Schultz, J., and Rahmann, S. 2004. HMM Logos for visualization of protein families. BMC Bioinformatics 5:7.
   Söding, J. 2005. Protein homology detection by HMM–HMM comparison. Bioinformatics 21:951‐960.
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