The Basics of Bioinformatics - MB150P88E

• Anglický název: The Basics of Bioinformatics
• Český název: Základy bioinformatiky
• Zajišťuje: Katedra buněčné biologie (31-151)
• Fakulta: Přírodovědecká fakulta
• Platnost: od 2024
• Semestr: letní
• E-Kredity: 5
• Způsob provedení zkoušky: letní s.:kombinovaná
• Rozsah, examinace: letní s.:2/2, Zk [HT]
• Počet míst: 65
• Minimální obsazenost: neomezen
• 4EU+: ne
• Virtuální mobilita / počet míst pro virtuální mobilitu: ne
• Stav předmětu: vyučován
• Jazyk výuky: angličtina
• Poznámka: povolen pro zápis po webu; při zápisu přednost, je-li ve stud. plánu
• Garant: Mgr. Marian Novotný, Ph.D.
• Vyučující: Mgr. Marian Novotný, Ph.D.
• Třída: Původní předmět
• Neslučitelnost : MB150P88
• Je neslučitelnost pro: MB150P88

Anotace

Laboratories around the world produce massive amount of new nucleotide and protein sequences, gene expression profiles,
3-D structures and other data of biological character. With an ever-increasing amount of data available, grows even
the significance of bioinformatics. Bioinformatics collects, archives and most importantly analyses and attempt to find a
meaning and useful information in this explosively growing sea of data. Bioinformatics is one of the most dynamically
developing areas of biomedical research and basic knowledge of bioinformatics methods becomes quickly indispensable for
anyone with a serious interest in doing biomedical research.
The aim of this course is to introduce students with basic, but also modern promising bioinformatics methods. These methods
will be shown and explained in lectures and later used in a series of practicals. These "hands-on" practicals are designed to
show how to take an advantage of bioinformatics in every day life in a laboratory. This course is suitable for the second- or higher year
students of biology or chemistry who want to specialize within the biomedical field of research. A basic knowledge of
structure of biomacromolecules (nucleic acids, proteins) is an advantage, but it is not required to have it. To successfully
finish the course, one has to attend the practicals and pass the final written exam.
The course has been modified to reflect a new study programme Parasitology and Infection Biology.

The course is taught with the support of the project ESF pro VŠ II na UK, Reg. num.: CZ.02.2.69/0.0/0.0/18_056/0013322

Poslední úprava: Novotný Marian, Mgr., Ph.D. (25.02.2021)

Literatura

Lesk, A. (2005): Introduction to bioinformatics, Oxford University Press, USA; 2 edition, 378 pp .

Baxevanis, A.D. & Ouellette B. F. F. (2004): Bioinformatics: Practical guide to the analysis of genes and proteins, Wiley-Interscience; 3 edition, 560 pp.

Bourne, P.E. & Weissig, H. (2003): Structural bioinformatics, Wiley-Liss, 649 pp.

Zvelebil & Baum (2008): Understending bioinformatics, Garland Science, USA, 772 pp.

Poslední úprava: Půta František, doc. RNDr., CSc. (22.02.2019)

Požadavky ke zkoušce

To obtain credits for Basics of Bioinformatics you need: 1) In collaboration with another student to write a short research of an important bioinformatics article. Points are awarded for the article, which are part of the final evaluation - article is not obligatory, but pounts to exam are awarded 3) Obtain at least 50% of points from the the total awarded for final written exam + article, where the student must answer the questions (not the test). The written exam lasts 2.5 - 3.5 hours.

Poslední úprava: Novotný Marian, Mgr., Ph.D. (25.02.2026)

Sylabus

1) Introduction to bioinformatics, overview of available methods
2) Data - how are they generated? (genomics, X-ray crystallography, cryo-em)
3) Data - where to find them? (databases)
4) Sequence alignment - algorithms, how to use it?
5) Looking for similar sequences - BLAST, PSI-BLAST

6) Structural alignment - algorithms, how to use it?
7) Analysis of protein structures
8) Prediction of  structures of proteins
9) Homology modelling

10)Tools for complex analysis of biological data
11) Phylogeny

Poslední úprava: Novotný Marian, Mgr., Ph.D. (25.02.2021)

Výsledky učení

Upon successful completion of the course, the student:

Professional Knowledge

• Explains the principles and limitations of experimental methods used to generate biological data (genomics, X-ray crystallography, microarray technology).

• Describes the fundamental algorithms used for global and local sequence alignment and the principles of scoring matrices.

• Defines the relationship between primary sequence and 3D protein structure within the context of structural bioinformatics.

• Clarifies the theoretical foundations of molecular evolution and the mathematical models used for phylogenetic tree construction.

Professional Skills

• Searches for and extracts relevant biological data from primary (GenBank, PDB, Uniprot) and specialized databases.

• Applies sequence analysis tools (BLAST, PSI-BLAST) to identify homologous sequences and functional domains.

• Analyzes protein structures using visualization software (Pymol) and performs structural alignments.

• Utilizes modern prediction methods, including homology modelling and AlphaFold, to generate hypothetical 3D protein models.

• Constructs a phylogenetic tree from a given set of sequences using an appropriate method.

General Competencies

• Interprets the results of bioinformatics analyses with regards to statistical significance (e.g., E-value).

• Critically evaluates the quality and reliability of predicted models in comparison with experimental data.

• Designs an appropriate bioinformatics pipeline to solve a specific biological problem based on available data.

Poslední úprava: Novotný Marian, Mgr., Ph.D. (04.02.2026)