Czech

Not applicable.

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
- program dotmatrix plot for nucleotide and aminoacid sequences and suitably select filtering parameters
- use alignment online tools and suitably choose scoring parameters according data type
- program algorithms for global and local alignment
- predict secondary structure of RNA sequences with online tools
- predict secondary structure of protein sequences with online tools
- program numerical representation of DNA sequences in 1. and 4. quadrant and compare the numerical signals by calculation of Eucledian distance
- program discrete Fourier transform for DNA sequences with fixed size of window and with moving window
- program calculation of DNA spectrograms
- construct phylogenetic tree from DNA sequences by online tools

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.

Not applicable.

Teaching methods depend on the type of the course unit as specified in the article 7 of BUT Rules for Studies and Examinations.

Student can get maximally:
30 points for programming,
30 points for test,
40 points for practical analysis.

1. Searching in sequence databases.
2. Prediction of protein coding regions and alignment of sequences.
3. Multialignment of sequences.
4. RNA secondary structure prediction.
5. Protein secondary structure prediction.
6. Numerical representations.
7. Discrete Fourier transform of DNA and protein sequences.
8. Spectrograms of DNA and protein sequences.
9. EIIP values for numerical representation and its spectrograms.
10. Phylogenetic tree construction.

Not applicable.

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.

Computer exercises are mandatory, properly excused missed lectures can be compensated individually after discussion with teacher.

Not applicable.

Not applicable.

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

Not applicable.