1-BIN-301, 2-AIN-501 Methods in Bioinformatics, 2023/24

Introduction · Rules · Tasks and dates · Materials · Moodle
Quizzes can be found in Moodle.
Homework assignments and journal club papers can be found in Tasks and dates.
Exam rules, example questions and syllabus
Groups for journal club have each their own group in Moodle.


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  • Lecture: Thursday 15:40-17:10 F1-109
  • Tutorial for computer science (BIN, INF, mINF, mAIN, DAV): Thursday 14:00-15:30 F1-109
  • Tutorial for biologists (PriFUK, physics): Thursday 17:20-18:50 M-217


Course objectives

This course is targeted at students of both computer science and life science study programs. Lectures will be together for both groups. Tutorials are held separately for CS and biology students.

  • Everyone: Overview of basic methods for analysis of biological sequences and other data sets in molecular biology.
  • CS: Algorithms and data structures, machine learning, probability. How to develop mathematical abstractions for real-world problems.
  • Biology: Mathematical models at the core of popular bioinformatics tools, how to use tools, interpretation of their results.
  • Everyone: Experience with interdisciplinary collaboration.

Brief syllabus

Basic concepts from molecular biology, algorithms and machine learning. Sequencing and assembling genomes. Gene finding. Sequence alignment. Evolutionary models and phylogenetic trees. Comparative genomics. RNA structure. Motif finding and gene expression analysis. Protein structure and function. Selected current topics.

Students of computer science programs will focus on computer science methods and mathematical modeling of the covered problems. Life science students will focus on understanding and correct application of these methods on real data.


Many basic concepts can be found in the following textbooks:

  • DEKM: Durbin, Eddy, Krogh, Mitchison: Biological sequence analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press 1998. Can be studied in the FMFI library under code I-INF-D-21
  • ZB: Zvelebil, Baum: Understanding Bioinformatics. Taylor & Francis 2008. Can be studied in the FMFI library under code I-INF-Z-2

The course material also draws on scientific literature and other materials.