| Time | Date | Teacher | Topics |
|---|---|---|---|
| Reading period week 1 | |||
| 13:15 | Monday 19 January | GK | Lecture: Introduction; Perl (1); Working with Linux |
| 15:15 | Monday 19 January | GK | Lecture: Introduction; Perl (1); Working with Linux (should finish early) |
| 08:00 | Thursday 22 January | GK | Lecture: Perl (2) |
| 10:00 | Thursday 22 January | GK | Practical 1: Perl (1) |
| Reading period week 2 | |||
| 08:00 | Thursday 29 January | GK | Lecture: Pairwise sequence alignment |
| 10:00 | Thursday 29 January | GK | Practical 2: Perl (2), Pairwise sequence alignment |
| 15:15 | Friday 30 January | MP |
Lecture: Markov chains
1 1.1-1.6 (optional), 2.1.1 |
| Reading period week 3 | |||
| 08:00 | Thursday 5 February | GK | Lecture: Perl (3) |
| 10:00 | Thursday 5 February | TS | Lecture: Molecular phylogeny |
| 15:15 | Friday 6 February | MP |
Lecture: Hidden Markov models (HMMs)
1 2.1.2-2.1.6 |
| Reading period week 4 | |||
| 08:00 | Thursday 12 February | GK | Lecture: Sequence alignment |
| 10:00 | Thursday 12 February | GK | Practical 3: Perl (3) |
| 15:15 | Friday 13 February | TÖ | Lecture: Next Generation Sequencing |
| Reading period week 5 | |||
| 08:00 | Thursday 19 February | GK | Lecture: More on Perl and sequence alignment |
| 10:00 | Thursday 19 February | GK | Practical 4: Perl (4) |
| Reading period week 6 | |||
| 08:00 | Thursday 26 February | TÖ | Lecture: Metagenomics |
| 10:00 | Thursday 26 February | TÖ | Practical 5: Resequencing analysis |
| 15:15 | Friday 27 February | MP |
Lecture: Training HMMs
1 6.1-6.5 |
| Reading period week 7 | |||
| 08:00 | Thursday 5 March | GK | Practical 6: Perl (5) |
| 10:00 | Thursday 5 March | MDL | Lecture: Identifying a disease causing mutation |
| 15:15 | Friday 6 March | MP |
Lecture: gHMM and profile HMMs
1 2.2, 3.1.2-3.1.5, 3.1.7, 3.2.9 |
| Reading period week 8 | |||
| 08:00 | Thursday 12 March | FB | Lecture: HMMER and applications; large-scale DNA sequence analysis |
| 10:00 | Thursday 12 March | GK/MP | Practical 7: Pairwise alignment and Perl revision; HMM exercises |
| 08:30 | Monday 16 March | Exam | |
1Axelsson-Fisk, M. (2010) Comparative Gene Finding: Models, Algorithms and Implementation, Springer.