Bulletin of Mathematical Biology

, Volume 68, Issue 2, pp 361–384

A Sufficient Condition for Reducing Recursions in Hidden Markov Models

Original Article

DOI: 10.1007/s11538-005-9045-9

Cite this article as:
Song, Y.S. Bull. Math. Biol. (2006) 68: 361. doi:10.1007/s11538-005-9045-9


In hidden Markov models, the probability of observing a set of strings can be computed using recursion relations. We construct a sufficient condition for simplifying the recursion relations for a certain class of hidden Markov models. If the condition is satisfied, then one can construct a reduced recursion where the dependence on Markov states completely disappears. We discuss a specific example—namely, statistical multiple alignment based on the TKF-model—in which the sufficient condition is satisfied.


Hidden Markov modelRecursionsReductionMarkov statesStatistical alignment

Copyright information

© Society for Mathematical Biology 2006

Authors and Affiliations

  1. 1.Department of StatisticsUniversity of OxfordOxfordUK
  2. 2.Department of Computer ScienceUniversity of California at DavisDavisUSA