The course main text book is "Biological Sequence Analysis" by Durbin et al.
The course is roughly divided among the following topics:
(including parameter estimation)
| Topic |
|---|
| Introduction to molecualr biology |
| Sequence alignment (global/local) |
Sequence alignment (FASTA/BLAST) |
Multiple alignment (DP and heuristic search) |
Markov models (theory + CpG island) |
HMM (viterbi, forward/backward, etc) |
HMM parameter estimation (Baum-Welch) |
| EM (Baum-Welch and ABO locus) |
| PPI (path queries) |
| Metabolic networks (OptKnock) |
| Phylogenetic trees (intro, MP/Fitch) |
| Phylogenetic trees (ML vs. MP, AML) |
| Phylogenetic trees (distance based methods) |