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Course, academic year 2023/2024
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The basis of Bioinformatics - MB150P88
Title: Základy bioinformatiky
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: 100
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Note: enabled for web enrollment
priority enrollment if the course is part of the study plan
Guarantor: Mgr. Marian Novotný, Ph.D.
Teacher(s): doc. Mgr. Vladimír Hampl, Ph.D.
Mgr. Marian Novotný, Ph.D.
Incompatibility : MB150P88E
Is incompatible with: MB150P88E
Annotation
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. To illustrate this fact, the number of known nucleotide sequences
grew from 59 millions to 80 millions last year (2006). The database of 3-D structures expanded by 20 % in the same year and
more than 1500 organisms are sequenced at the moment. 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. The practicals were tested for a long time
and successfully on students of the Uppsala university, Sweden. 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.
Last update: PUTA (15.04.2007)
Aim of the course - Czech

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.

Last update: Novotný Marian, Mgr., Ph.D. (26.10.2011)
Literature

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.

Last update: Novotný Marian, Mgr., Ph.D. (09.11.2011)
Requirements to the exam
To obtain credits for Basics of Bioinformatics you need:
1) Give answers to questions from all exercises
2) 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
3) Obtain at least 50% of points from the final written exam, where the student must answer the questions (not the test). The written exam lasts 2.5 - 3.5 hours.
Last update: Novotný Marian, Mgr., Ph.D. (25.02.2021)
Syllabus

1) Introduction to bioinformatics, overview of available methods

2) Data - how are they generated? (genomics, X-ray crystallography, microarray technology)

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 3-D structures of proteins

9) Homology modelling and drug design

10) Prediction of genes

11) Phylogeny

12) Microarray data analysis

Last update: Novotný Marian, Mgr., Ph.D. (16.02.2012)
 
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