The course main text book is "Biological Sequence Analysis" by Durbin et al. The course is roughly divided among the following topics
|
Topic |
Reading |
#weeks |
|
Introduction |
Setubal & Meidanis, chapter 1 |
1 week |
|
Sequence alignment
(including parameter estimation) |
Durbin et al., chapters 2, 1.3, 11.3
Setubal & Meidanis, chapter 3.5
Polanski & Kimmel, chapter 6 |
3 weeks |
|
Markov chains and HMMs |
Durbin et al., chapter 3
Polanski & Kimmel, chapters 2.8, 2.10 |
3 weeks |
|
The EM algorithm |
Durbin et al., chapters 11.2, 11.6
Polanski & Kimmel chapter 2.6 |
2-3 weeks |
|
Phylogenetic trees |
Durbin et al., chapters 7.1-7.3, 7.8, 3.7, 8.1
Polanski & Kimmel, chapter 7 |
2-3 weeks |
Technion - Israel Institute of Technology 
