#DOTD: profile Hidden Markov model

19 Jun 2017

A profile Hidden Markov model (profile-HMM) is an acyclic linear HMM that contains three types of states: match, insert and delete, corresponding to symbol frequencies, insertions and deletions, respectively.


The information needed to build profile-HMMs is from Multiple Sequence Alignments (MSAs) of protein families. The use of profile-HMMs, therefore, is in modelling protein families to allow for efficient querying of unannotated protein sequences.


The below diagram shows how profile-HMMs are built from MSAs.


 This blog post is based on the following paper:


Yoon, B.J., 2009. Hidden Markov models and their applications in biological sequence analysis. Current genomics, 10(6), pp.402-415.




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