| Time | Date | Teacher | Topics |
|---|---|---|---|
| Reading period week 1 | |||
| 13:15 | Monday 18 January | GK | Lecture: Introduction; Perl (1); Working with Linux |
| 15:15 | Monday 18 January | GK | Lecture: Introduction; Perl (1); Working with Linux (should finish early) |
| 08:00 | Thursday 21 January | GK | Lecture: Perl (2) |
| 10:00 | Thursday 21 January | GK | Practical 1: Perl (1) |
| Reading period week 2 | |||
| 08:00 | Thursday 28 January | GK | Lecture: Pairwise sequence alignment |
| 10:00 | Thursday 28 January | GK | Practical 2: Perl (2), Pairwise sequence alignment |
| 15:15 | Friday 29 January | MP |
Lecture: Markov chains
(local access only)
1 1.1-1.6 (optional), 2.1.1 |
| Reading period week 3 | |||
| 08:00 | Thursday 4 February | GK | Lecture: Perl (3) |
| 10:00 | Thursday 4 February | TS | Lecture: Molecular phylogeny |
| 15:15 | Friday 5 February | MP |
Lecture: Hidden Markov models (HMMs)
(local access only)
1 2.1.2-2.1.6 |
| Reading period week 4 | |||
| 08:00 | Thursday 11 February | GK | Lecture: Sequence alignment |
| 10:00 | Thursday 11 February | GK | Practical 3: Perl (3) |
| 15:15 | Friday 12 February | TÖ | Lecture: Next Generation Sequencing |
| Reading period week 5 | |||
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| 08:00 | Thursday 18 February | TÖ | Lecture: Metagenomics |
| 10:00 | Thursday 18 February | TÖ | Practical 4: Resequencing analysis |
| Reading period week 6 | |||
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| 08:00 | Thursday 25 February | GK | Lecture: More on Perl and sequence alignment |
| 10:00 | Thursday 25 February | GK | Practical 5: Perl (4) |
| 15:15 | Friday 26 February | MP |
Lecture: Training HMMs
(local access only)
1 6.1-6.5 |
| Reading period week 7 | |||
| 08:00 | Thursday 3 March | GK | Practical 6: Perl (5) |
| 10:00 | Thursday 3 March | MDL | Lecture: Identifying a disease causing mutation |
| 11:00 | Thursday 3 March | MP | Exercises: HMMs |
| 15:15 | Friday 4 March | MP |
Lecture: Pair HMMs
(local access only)
1 3.1.7 |
| Reading period week 8 | |||
| 08:00 | Thursday 10 March | FB | Lecture: HMMER and applications; large-scale DNA sequence analysis |
| 10:00 | Thursday 10 March | GK/MP | Practical 7: Perl (6); HMMs |
| 08:30 | Monday 14 March | Exam | |
1Axelsson-Fisk, M. (2010) Comparative Gene Finding: Models, Algorithms and Implementation, Springer.