Czech

Not applicable.

Student should have knowledge equivalent to completion of the course ABIN. Student should be able to work with Matlab or other programming language. Student have to know the basics of molecular biology of nucleotide and protein sequences and understand to principles of global and local sequence alignment and principle of protein secondary structure prediction.

Student can get maximally 30 points for programming, maximally 30 points for practical work and maximally 40 points for theoretical test. It is necessary to get minimally 15 points for the programming, minimally 20 points for the theoretical test and minimally 50 points in sum to successfully pass the course.
Computer exercises are mandatory, properly excused missed lectures can be compensated individually after discussion with teacher.

The goal of this course is to teach the students how to search in the basic genomic and proteomic databases like GenBank and Uniprot, analyse data from the databases with commonly used bioinformatic online tools, and the student are also teached how to program some basic bioinformatics algorithms in R programming language.
The student is able to:
- find protein-coding DNA sequences in GenBank database and load the data in desired format
- find protein sequence, which is coded by the DNA sequence, in Uniprot database
- find coding regions in DNA sequences
- analyse sequences in R
- use alignment online tools and suitably choose scoring parameters according data type
- program algorithms for alignment with afinne penalty
- predict secondary structure of protein sequences with online tools
- predict positive selection in genes
- program calculation of DNA spectrograms
- construct phylogenetic tree from DNA sequences by online tools

Not applicable.

Not applicable.

Cvrčková F: Úvod do praktické bioinformatiky, Academia, 2006 (CS)

Not applicable.