IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

Fakulta informatiky
podzim 2008
Rozsah
1/1/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.
Vyučující
Dr. Ingo Ebersberger (přednášející), doc. Ing. Matej Lexa, Ph.D. (zástupce)
Dr. Greg Ewing (přednášející), doc. Ing. Matej Lexa, Ph.D. (zástupce)
Garance
prof. Ing. Václav Přenosil, CSc.
Katedra strojového učení a zpracování dat – Fakulta informatiky
Kontaktní osoba: doc. Ing. Matej Lexa, Ph.D.
Rozvrh
Pá 12:00–15:50 B117
Předpoklady
Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themself familiar with the linux operating system.
Omezení zápisu do předmětu
Předmět je nabízen i studentům mimo mateřské obory.
Mateřské obory/plány
předmět má 39 mateřských oborů, zobrazit
Cíle předmětu
The assumption that all species, extant and extinct, evolved from a single common ancstor species forms the basis of phylogenetic research. By comparing both DNA and protein sequences, it is one key aspect of applied bioinformatics to reconstruct when and in which order the corresponding species have emerged. In this course we will detail on our current understanding of how biological sequences change over time. We will present methods to infer a phylogenetic tree from DNA and protein sequences and how to test the significance of this reconstruction. Particular attention will be given to how to compile an informative data set from the millions of different sequences available in the public databases. Eventually, we will discuss to what extent the evolution of biological sequences is informative for the evolution of species. The course will cover both a theory part and practical exercises where the students will have hands-on training on phylogeny reconstruction in a computer lab.
Osnova
  • The course will deal with the following topics: 1) The molecular basis of evolution. A primer of molecular genetics. 2) Introduction into basic population genetics and the coalescent model. 3) Modelling sequence evolution. 4) Methods for phylogenetic tree reconstruction. Maximum Parsimony, Maximum Likelihood, Bayesian Inference. 5) Biological Sequence databases
Literatura
  • ZVELEBIL, Marketa J. a Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info
  • PAGE, Roderic D. M. a Edward C. HOLMES. Molecular evolution :a phylogenetic approach. Oxford: Blackwell Science, 1998, v, 346 s. ISBN 0-86542-889-1. info
Metody hodnocení
exercices and written exam
Vyučovací jazyk
Angličtina
Informace učitele
http://www.cibiv.at/
ATTENTION! This course will be taught as a block of lectures and exercises in the period Nov - Dec, mostly on Fridays and Saturdays.
Předmět je zařazen také v obdobích podzim 2007, podzim 2009, podzim 2010, podzim 2011.