Computational Molecular Biology, aka Algorithms for Computational Biology

Profile Hidden Markov Model Module Guide

This module is intended to teach you about one of the more important applications of hidden Markov models in genomic sequence analysis: identification of conserved functional domains in protein sequences. Specifically, you should be able to:

  1. Use profile HMMs to identify domains in protein sequences via the PFAM website.
  2. Explain how parameters for a profile HMM can be estimated from a multiple sequence alignment for a domain and do it by hand.
  3. Draw the generic state diagram of a profile HMM and explain how it is a special case of a generic HMM.
  4. Carry out the profile version of Viterbi decoding by hand and/or implement it on a computer.

The source for the material in this module is largely Chapter 5 of Biological Sequence Analysis, (BSA) by Durbin et al.

Day 0
Before the first class

Day 1
In class

Before class on Day 3
Day 2
In class
Before the next class
Day 3
In class
Before class on Day 1 of the next module
Day 4
In class
Before the next class