APPENDIX 3A An Introduction to Hidden Markov Models

  1. Benjamin Schuster-Böckler,
  2. Alex Bateman

Published Online: 1 JUN 2007

DOI: 10.1002/0471250953.bia03as18

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Schuster-Böckler, B. and Bateman, A. 2007. An Introduction to Hidden Markov Models. Current Protocols in Bioinformatics. 18:3A:A.3A.1–A.3A.9.

Author Information

  1. Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom

Publication History

  1. Published Online: 1 JUN 2007
  2. Published Print: JUN 2007


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.


  • Markov Chains;
  • HMM;
  • hidden Markov Models;
  • Machine Learning;
  • Sequence Analysis