Algorithms in computational genomics
General data
Course ID: | 1000-2M12AGO |
Erasmus code / ISCED: |
11.3
|
Course title: | Algorithms in computational genomics |
Name in Polish: | Algorytmy w genomice obliczeniowej (wspólne z 1000-719GP2) |
Organizational unit: | Faculty of Mathematics, Informatics, and Mechanics |
Course groups: |
Elective courses for Computer Science Elective courses for Machine Learning |
ECTS credit allocation (and other scores): |
(not available)
|
Language: | English |
Type of course: | elective monographs |
Short description: |
The main aim of this lecture is to introduce students with selected models, algorithms and tools used in comparative genomics. In particular we will be focused on algorithms and tools related to trees (in many contexts). Classes will be partially converted to labs. |
Full description: |
1. Introduction. Elementary defintions, genes, species, genomes, ewolution, alignments, sequence comparison (2 lectures). 2. Models of sequence evolution (1). 3. Maximum likelihood estimation, maximum parsimony, nearest neighbor joining (2) 4. Bayes methods (1-2) 5. Consesus trees and supertrees (2) 6. Hierarchical clustering (1) 7. Reconciled trees, networks, horizontal transfer (2-3). 8. Suffix trees, suffix arrays (1-2). Założenia Basics of algorithmics, programming skills (e.g. python, c/c++ or java) |
Bibliography: |
1. Inferring Phylogenies Joseph Felsenstein 2. Paul G. Higgs, Teresa K. Attwood, Bioinformatyka i ewolucja molekularna, 3. R. Durbin, S. Eddy, A. Krogh, G. Mitchson, Biological Sequence Analysis, . |
Learning outcomes: |
Has knowledge on advanced methods from comparative genomics (K_W04) can perform computations related to genome comparison and can interpret their results (K_U07) |
Assessment methods and assessment criteria: |
Exam 60% + compulsory lab project 35% + project presentation 5%. |
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