Course detail

Analysis of Biological Sequences

FEKT-MPCN-ABSAcad. year: 2026/2027

The course focuses on advanced methods for processing biological sequences. It assumes that students have already mastered core bachelor‑level bioinformatics topics, including the acquisition and storage of biological sequences, their interconversion, and basic techniques for comparing two or more sequences.

Students will explore advanced representations of biological sequences and mathematical models that describe the effects of mutation and evolutionary processes in DNA and protein sequences. The course also introduces fundamental approaches to phylogenetic tree reconstruction and their statistical evaluation.

A substantial portion of the course is dedicated to handling large‑scale data generated by second‑ and third‑generation sequencing technologies. Topics include genome assembly, assessment of genetic variability, detection of structural variants, and the analysis of microbial data.

 

Language of instruction

Czech

Number of ECTS credits

5

Mode of study

Not applicable.

Guarantor

Ing. Helena Vítková, Ph.D.

Department

Department of Biomedical Engineering (UBMI)

Entry knowledge

The student should be able to explain fundamental principles of genetics, should know basic terms and laws of molecular biology and should be oriented in basic knowledge of digital signal processing. In general, knowledge on the Bachelor's degree level is requested.

 

Rules for evaluation and completion of the course

To receive credit, students must earn at least 20 points from all scoring activities during the semester:
-Ongoing knowledge tests: 2 × 12 points (maximum 24 points)
-Team project: maximum 16 points

Exercises are obligatory, one absence is allowed. Other absences are only possible for medical reasons, immediately excused (by a doctor's certificate). Compensation for uncompleted exercise is possible in the last week of semester. Only students with a credit can take the final oral exam.

To successfully complete the course, it is necessary to obtain at least 30 points from the final exam. The final score is determined from the points obtained during the semester (max. 40 points) and the final exam (max. 60 points).

 

Aims

The aim of the course is to provide knowledge about advanced methods for analysis of biological sequences based on deterministic as well as stochastic approach.
The student will be able to:
- describe basic methods of computer processing of symbolic sequences,
- explain characteristics of DNA and protein evolution,
- describe principle of methods for construction and analysis of phylogenetic trees,
- explain principle of numeric conversion of symbolic biological sequences.
- select and set up the right tool for assembling genomes for different applications
- evaluate the genetic variability of microbial genomes,
- discuss the advantages and disadvantages of individual methods.

 

Study aids

Not applicable.

Prerequisites and corequisites

Not applicable.

Basic literature

Amjesh, R. Bioinformatics for beginners. LAP LAMBERT Academic Publishing, 2019. ISBN 978-6200262851
Srinivasa, K. G. Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications. Springer, 2020. ISBN 978-9811524448

Recommended reading

Not applicable.

Classification of course in study plans

  • Programme MPCN-BTB Master's 1 year of study, summer semester, compulsory, profile core courses

Type of course unit

 

Lecture

26 hours, compulsory

Teacher / Lecturer

Ing. Helena Vítková, Ph.D.

Syllabus

  1. Genetic variability
  2. Models of DNA evolution
  3. Models of protein evolution
  4. Phylogenetic trees Introduction
  5. Phylogenetic trees - construction
  6. Evaluation of phylogenetic analysis 
  7. Numerical and graphical representations  
  8. Description of protein structure
  9. Comparison of protein structures
  10. Sequencing data entry
  11. Sequencing data processing
  12. Analysis of microbial data from NGS
  13. Detection of structural changes of the genome

Exercise in computer lab

26 hours, optionally

Teacher / Lecturer

Ing. Helena Vítková, Ph.D.

Syllabus

  1. Genetic variability, motifs, and sequence logos
  2. Models of DNA, protein, and codon sequence evolution
  3. Methods for constructing, evaluating the quality of, and interpreting phylogenetic trees
  4. Numerical representations and digital signal processing of genomic signals
  5. Methods for recording and evaluating the stereochemical quality of tertiary protein structures
  6. Methods for evaluating the mutual similarity of tertiary protein structures
  7. Recording, compiling, and evaluating the quality of sequencing data
  8. Detection of structural changes in bacterial genomes
  9. Team projects I – division into teams and assignment of tasks
  10. Team projects II. – briefing and consultation on the project
  11. Team projects III. – briefing and consultation on the project
  12. Team projects IV. – briefing and consultation on the project
  13. Team projects V. – presentation of results and defense of projects
 

Project

10 hours, compulsory

Teacher / Lecturer

Ing. Helena Vítková, Ph.D.

Syllabus

Work on a group project (groups of 1-3 members) - 5 weeks of the semester. 

Regular individual preparation for activities in the semester

33 hours, optionally

Teacher / Lecturer

Ing. Helena Vítková, Ph.D.

Syllabus

Regular individual preparation during the semester includes:
- theoretical preparation for exercises
- completing interactive exercises
- studying for ongoing tests
- working on team projects outside of scheduled classes 

Individual preparation for a final exam

26 hours, optionally

Teacher / Lecturer

Ing. Helena Vítková, Ph.D.

Syllabus

Final preparation for the oral exam based on the study materials provided (presentations for lectures and exercises), your own notes, and interactive documents with program codes for computer exercises. Alternatively, from basic literature.