IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

Faculty of Informatics
Autumn 2011
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 12:00–13:50 C525
Prerequisites
Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themselves 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
Course objectives
In this course we will detail on our current understanding of how biological sequences change over time.
At the end of the course, the student will:
be able to use methods to infer a phylogenetic tree from DNA and protein sequences
know how to test the significance of phyllogenetic tree reconstruction
be able to extract useful datasets from sequences available in the public databases
understand the difference between evolution of biological sequences and the evolution of species
Syllabus
  • The course will deal with the following topics:
  • The molecular basis of evolution. A primer of molecular genetics.
  • Introduction into basic population genetics and the coalescent model.
  • Modelling sequence evolution.
  • Methods for phylogenetic tree reconstruction. Maximum Parsimony, Maximum Likelihood, Bayesian Inference.
  • Biological Sequence databases
Literature
  • 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
  • ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info
Teaching methods
lectures and computer exercises
Assessment methods
exercises and written exam
Language of instruction
English
Further comments (probably available only in Czech)
Study Materials
Teacher's information
http://www.cibiv.at/
The course is also listed under the following terms Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010.
  • Enrolment Statistics (recent)
  • Permalink: https://is.muni.cz/course/fi/autumn2011/IV116