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Pair hidden Markov models

Part 4. Bioinformatics

4.2. Gene Finding and Gene Structure

Specialist Review

  1. Marina Alexandersson,
  2. Nicolas Bray,
  3. Lior Pachter

Published Online: 15 JUL 2005

DOI: 10.1002/047001153X.g402215

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Alexandersson, M., Bray, N. and Pachter, L. 2005. Pair hidden Markov models. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.2:17.

Author Information

  1. University of California Berkeley, Berkeley, CA, USA

Publication History

  1. Published Online: 15 JUL 2005

Abstract

We describe pair hidden Markov models, with an emphasis on their relationship to evolutionary models and hidden Markov models. We then explain the statistical interpretation of alignment with pair hidden Markov models, and highlight connections to the Needleman–Wunsch algorithm and other dynamic programming–based alignment algorithms.

Keywords:

  • alignment;
  • dynamic programming;
  • evolutionary models;
  • graphical models;
  • pair hidden Markov models