Apart from lecture- and practical- specific reading the following are of general relevance to this part of the module.
| Time and Place | Title | Reading | Practical/Problem class |
| RCH/017 1015 10 Jan | Multiple alignments, families of sequences and profile hidden Markov models | Chapter 1 of HMMER User guide | |
| RCH/017 1415 10 Jan | Profile HMMs for ungapped regions of a multiple alignment | First 3.5 pages of chapter 5 of Durbin et al | |
| RCH/017 1015 12 Jan | Profile HMMs for multiple alignments with gaps | HERE |
RCH/018 1015 16 Jan HMMer tutorial |
| RCH/017 0915 18 Jan | Estimation of probabilities | RCH/018 1615 24 Jan Estimating probabilities | |
| RCH/042 1015 23 Jan | Forward and backward probabilities in HMMs | RCH/018 1015 30 Jan HMMs1 |
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| RCH/017 1115 24 Jan | The Viterbi and Baum-Welch algorithms for HMMs | RCH/018 1115 31 Jan HMMs2 |
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| RCH/042 1015 6 Feb | Significance of hits. Local and global alignment with HMMER |