Comparative genomics 1000-719GP2
1. Basic notions: genes, species, genomes, evolution, multiple alignments, comparing sequences.
2. Models of sequence evolution.
3. Tree inference: maximum likelihood, maximum parsimony, neighbor-joining.
4. Bayesian methods.
5. Clustering of molecular sequences
6. Hierarchical clustering.
7. Bootstrapping.
8. Consensus trees.
9. Supertrees.
10. Reconciled trees.
11. Phylogenetic networks.
Course coordinators
Type of course
Learning outcomes
has knowledge of advanced methods used in comparative genomics
can perform calculations related to comparing genomes and interpret their results
Assessment criteria
A maximum of 100 points is available: tests — 20 points, project — 20 points, written examination — 60 points.
1. Laboratory assignments: students must complete and submit at least 6 of the 13 assignments by their deadlines, including three designated assignments that require an in-person presentation and successful assessment. The remaining submitted assignments will be assessed offline. Assignments do not carry separate points.
2. Tests: two 45-minute tests assessing understanding of the laboratory assignments, worth 10 points each, will take place in late November and January. The announced scope applies to everyone, regardless of the assignments selected for submission. A common resit date will be provided; the higher score for each test counts.
3. Project: the core component is worth 14 points, with two optional extensions worth 3 points each. Passing requires at least 8 points from the core component and a successful in-person presentation and defence. Extension points cannot replace the required minimum.
4. Final grade: passing requires fulfilment of the laboratory and project requirements and at least 60 points overall. Grade thresholds: 60–<65 points — 3.0; 65–<70 — 3.5; 70–<75 — 4.0; 75–<80 — 4.5; 80 or more — 5.0.
5. Early assessment option (“term zero”): eligibility requires successful completion of the required assignments and presentations, at least 5/10 on each test, and a project submitted on time and successfully defended during the final class. The proposed grade is based on up to 40 points from the tests and project; separate thresholds will be announced before the first test. Students may decline the proposed grade and take the written examination.
6. Independent work: AI assistance when preparing solutions is permitted unless an assignment specifies otherwise; the extent of its use must be disclosed. Students are responsible for their solutions and must understand them. Tests and individual verification take place without AI assistance or help from others.
Bibliography
1. Joseph Felsenstein, Inferring Phylogenies
2. Paul G. Higgs, Teresa K. Attwood, Bioinformatics and Molecular Evolution
3. R. Durbin, S. Eddy, A. Krogh, G. Mitchson, Biological Sequence Analysis.
Additional information
Information on level of this course, year of study and semester when the course unit is delivered, types and amount of class hours - can be found in course structure diagrams of apropriate study programmes. This course is related to the following study programmes: