Applications of DNA analysis

Goal: Knowing and understanding the basic concepts and definition relevant to bioinformatics. Knowing and understanding the bioinformatics methods of DNA analyses, and acquiring the skill of their application in various fields of life sciences. Acquiring the skill of the use of computer techniques in bioinformatics. Knowing the bioinformatic databases and their functioning.

ECTS points in relation to student’s duties

1 ECTS pt – 30 class participation hours

2 ECTS pt – 25 hours of consultation and/or exercise preparation for in-class discussion; 25 hours of exercises as take-home assignments.

Preliminary conditions: Computer skills and elementary knowledge of computer science and IT, a basic knowledge on the principles of organisms systematics and classification, genetics and evolution, an ability to find and process biological information into knowledge, an ability to use the relevant published biological scientific literature and to know its practical application.

Lecture: Essential bioinformatics. Molecular databases as sources of DNA sequences used in various fields of life sciences. Analyses of mitochondrial and nuclear DNA. DNA polimorphism. Molecular markers in phylogenomics, phylogeography, ecology, conservation biology, forensic biology, medicine and biodiversity studies. Application of bioinformatic methods in studies on fossils. Basics of the structural bioinformatics Computer programms enabling the use of bioinformatic data in various fields of life sciences.

Laboratory: Computer programms and bioinformatic databases in phylogenomic and phylogeographic analyses. Haplotype analyses. Procedures of downloading the DNA sequences from GenBank. Sequence alignments and analyses. Substitution model selection. Tree construction using different algorithms. Presentation of results of computer analyses and simulations.

Didactic methods

Multimedial lecture (e-learning on the platform Moodle).

Laboratory: exercises involving computer programs and internet data, computer simulations, discussion, work in focus groups.

Avise J.C. Phylogeography: the history and formation of species. Harvard University Press, 2001.

Freeland J.R. Molecular ecology. John Wiley & Sons Ltd., 2005.

Hall B.G. Phylogenetic trees made easy: A how-to manual. Third edition. Sinauer Associates Inc., 2008.

Higgs P.G., Attwood T.K. Bioinformatics and Molcular Evolution. Blackwell Science Ltd., 2005.

Xiong J. Essential bioinformatics. Cambridge University Press, 2006.

Basic criteria:

Lecture: positive rating over 50% of points scored (in the final test)

Laboratory: evaluation of results obtained during computer analyses

Form of testing:

Lecture: final written test (including open and closed questions)

Laboratory oral presentation of results of computer analyses and simulations (accompanied by the electronic presentation).