Hidden Markov Models and their Applications in Biological Sequence Analysis

Byung-Jun Yoon
2009 Current Genomics  
Hidden Markov models (HMMs) have been extensively used in biological sequence analysis. In this paper, we give a tutorial review of HMMs and their applications to a variety of problems in molecular biology. We especially focus on three types of HMMs: the profile-HMMs, pair-HMMs, and context-sensitive HMMs. We show how these HMMs can be used to solve various sequence analysis problems, such as pairwise and multiple sequence alignments, gene annotation, classification, similarity search, and many
more » ... others. Index Terms Hidden Markov model (HMM), pair-HMM, profile-HMM, context-sensitive HMM (csHMM), profile-csHMM, sequence analysis.
doi:10.2174/138920209789177575 pmid:20190955 pmcid:PMC2766791 fatcat:h6m33ccye5h27hdzk6z27khpki