Course detail

Bioinformatics

FEKT-BPC-BINAcad. year: 2025/2026

The course is dedicated to the principles of bioinformatics work with biological sequences. It is focused on acquiring knowledge about biological databases, their structure, and possible applications. It emphasizes the study of informatics methods applicable in the analysis of sequences from biological databases, including DNA, as well as the study of the concepts of genomics and proteomics. Students will gain practical experience with the Python programming language, which will be used for designing algorithms for the acquisition and processing of biological sequences. 

Language of instruction

Czech

Number of ECTS credits

5

Mode of study

Not applicable.

Guarantor

Ing. Markéta Jakubíčková, Ph.D.

Department

Department of Biomedical Engineering (UBMI)

Entry knowledge

The student should be able to explain the basic principles of classical genetics, be familiar with fundamental concepts and laws of molecular biology, and have basic knowledge of digital signal processing. In general, knowledge at the high school level is required. Additionally, the student should have proficiency in programming in the Python language. 

Rules for evaluation and completion of the course

During the semester, students can earn up to 20 points from tests in exercises. At the end of the semester, students take a credit test, which can yield a maximum of 20 points. The final exam is in written form, with a maximum score of 60 points.

Further details are provided in the updated regulations issued by the course guarantor before the start of the respective semester.

 

Aims

The aim of the course is to inform students about bioinformatics, namely about information structure in biological databases and way of their use and about methods of analysis of sequences acquired from biological databases.
The student will be able to:
- acquire information from biological databasis,
- explain fundamental terms of bioinformatics,
- describe principle of basic methods for analysis of sequences from biological databases,
- discus advantages and disadvantages of the methods,
- design custom methods for sequence analysis based on defined requirements.

Study aids

Not applicable.

Prerequisites and corequisites

Not applicable.

Basic literature

LESK, Arthur, 2019. Introduction to bioinformatics. Oxford University Press. ISBN 978-019-8794-141 (EN)
PEVSNER, Jonathan, 2015. Bioinformatics and functional genomics. Third edition. Chichester: Wiley-Blackwell. ISBN 978-1-118-58178-0 (EN)

Recommended reading

Not applicable.

Classification of course in study plans

  • Programme BPC-BTB Bachelor's 2 year of study, summer semester, compulsory, profile core courses

Type of course unit

 

Lecture

26 hod., optionally

Teacher / Lecturer

Ing. Markéta Jakubíčková, Ph.D.
Ing. Helena Vítková, Ph.D.
doc. Mgr. Ing. Karel Sedlář, Ph.D.

Syllabus

1. Introduction to Bioinformatics, Basics of Molecular Biology
2. Basics of Sequencing, Sequencing Platforms
3. Processing of Sequencing Data
4. Dynamic Programming
5. Algorithms for Aligning Biological Sequences 1
6. Algorithms for Aligning Biological Sequences 2
7. Mutations and Substitution Matrices
8. BLAST and Multiple Sequence Alignment
9. Introduction to Phylogenetics, Phylogenetic Trees, and Methods of Their Construction
10. Numerical Representations of Sequences
11. Proteins and Methods for Protein Structure Prediction 

Exercise in computer lab

26 hod., compulsory

Teacher / Lecturer

Ing. Markéta Jakubíčková, Ph.D.
Ing. Kristýna Heřmánková

Syllabus

1. Introduction to Molecular Biology, Review of Python Basics
2. Data Formats in Bioinformatics
3. Working with Sequencing Data
4. LCS and Edit Distance
5. Global Sequence Alignment
6. Local Sequence Alignment
7. Scoring and Substitution Matrices
8. Multiple Sequence Alignment, BLAST
9. Phylogenetic Tree Construction
10. Numerical Representations of Sequences
11. Signal Processing of Bioinformatics Data
12. Protein Structure Prediction