IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

Faculty of Informatics
Autumn 2008
Extent and Intensity
1/1/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Teacher(s)
Dr. Ingo Ebersberger (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)
Dr. Greg Ewing (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)
Guaranteed by
prof. Ing. Václav Přenosil, CSc.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.
Timetable
Fri 12:00–15:50 B117
Prerequisites
Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themself familiar with the linux operating system.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 39 fields of study the course is directly associated with, display
Course objectives
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.
Syllabus
  • 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
Literature
  • ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info
  • PAGE, Roderic D. M. and Edward C. HOLMES. Molecular evolution :a phylogenetic approach. Oxford: Blackwell Science, 1998, v, 346 s. ISBN 0-86542-889-1. info
Assessment methods
exercices and written exam
Language of instruction
English
Teacher's information
http://www.cibiv.at/
The course is also listed under the following terms Autumn 2007, Autumn 2009, Autumn 2010, Autumn 2011.
  • Enrolment Statistics (Autumn 2008, recent)
  • Permalink: https://is.muni.cz/course/fi/autumn2008/IV116