The basics of Bioinformatics - MB150P88E

• Title: The basics of bioinformatics
• Czech title: Základy bioinformatiky
• Guaranteed by: Department of Cell Biology (31-151)
• Faculty: Faculty of Science
• Actual: from 2021
• Semester: summer
• E-Credits: 5
• Examination process: summer s.:combined
• Hours per week, examination: summer s.:2/2, Ex [HT]
• Capacity: 65
• Min. number of students: unlimited
• 4EU+: no
• Virtual mobility / capacity: no
• State of the course: taught
• Language: English
• Note: enabled for web enrollment; priority enrollment if the course is part of the study plan
• Guarantor: Mgr. Marian Novotný, Ph.D.
• Teacher(s): Mgr. Marian Novotný, Ph.D.
• Class: Původní předmět
• Incompatibility : MB150P88
• Is incompatible with: MB150P88

Annotation

Last update: Mgr. Marian Novotný, Ph.D. (25.02.2021)

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

Aim of the course

Last update: doc. RNDr. František Půta, CSc. (22.02.2019)

Cílem předmětu je poskytnout přehled o základních bioinformatických metodách, které lze použít v každodení vědecké práci. Jde o velmi prakticky zaměřený kurz, který kombinuje přednášky, cvičení a aktivní práci s literaturou za účelem seznámení se s dostupnými bioinformatickými možnostmi. Nejde tedy primárně o kurz pro budoucí bioinformatiky, ale spíše pro biology, chemiky, kteří mohou narazit při svém výzkumu na potřebu analyzovat a srovnávat svůj protein, gen, organismus s dalšími daty.

Literature

Last update: doc. RNDr. František Půta, CSc. (22.02.2019)

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.

Requirements to the exam

Last update: Mgr. Marian Novotný, Ph.D. (14.01.2021)

The requirements for passing the course:

1) to hand in the answers to the questions in all exercises

2) to write in a cooperation with other student a short essay about seleected scientific article. The essay will be evaluated and it is a part of a final grade

3) to pass the exam and acquire at least 50% of available points in total

Syllabus

Last update: Mgr. Marian Novotný, Ph.D. (25.02.2021)

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