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.
Groups for journal club have each their own group in Moodle.


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This webpage contains a preliminary schedule of lectures and tutorials for the semester which will be updated as needed. Notes and presentations will be published after each class.


  • BV: Brejová, Vinař: Metódy v bioinformatike. (preliminary version of lecture notes in Slovak, only several lectures) pdf
  • 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

For each lecture, we list book chapters best corresponding to the covered material. However, the lecture may differ substantially from the listed chapters which serve as the source of additional information.

Recordings of lectures in Slovak from 2018/19

Notes and presentations

L: lecture (everybody), TI: tutorial for computer science/informatics students, TB: tutorial for biology/chemistry/physics students

Week 1, Week 2, Week 3, Week 4, Week 5, Week 6, Week 7, Week 8, Week 9, Week 10, Week 11, Week 12, Week 13

Sept. 23
L: Introduction, course rules, sequencing and genome assembly pdf, pdf
BV chapter 1, SK video 1 SK video 2
TI: Introduction to biology pdf SK notes
ZB chapter 1, SK video
TB: Introduction to computer science, UCSC genome browser pdf SK notes
Sept. 30
L: Genome assembly 2 pdf
SK video
TI: Introduction to probability, genome coverage by sequencing reads pdf (SK) SK notes
TB: Introduction to dynamic programming, introduction to probability pdf SK notes
Oct. 7
L: Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring pdf
BV chapter 2, DEKM chapter 2.1-2.4, 2.8, ZB chapter 4.1-4.4, 5.1-5.2, SK video
TI: Introduction to dynamic programming, proteomics pdf (SK) notes
TB: Dynamic programming for sequence alignment, dotplots pdf notes
Oct. 14
L: Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments pdf
BV chapter 2, DEKM chapter 2.5, 2.7, 6.1-6.3; ZB chapter 4.5-4.7, 5.3-5.5, SK video
TI: Advanced algorithms for sequence alignment SK notes
TB: Programs for sequence alignment, scoring schemes SK notes
Oct. 21
L: Gene finding, hidden Markov models pdf
BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7, SK video
TI: Fast similarity search, BLAST, MinHash SK notes
TB: Hidden Markov models, E-value pdf SK notes
Oct. 28
L: Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) pdf
BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2, SK video
TI: Algorithms for HMM pdf SK notes
TB: Substitution models, bootstrap, tree rooting pdf SK notes
Nov. 4
L: Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs pdf
BV chapter 5, ZB chapter 9.8, 10.8, SK video
TI: Substitution models pdf SK notes
TB: Phylogenetic trees pdf, pdf SK notes
Nov. 11
L: Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs pdf
DEKM chapter 5.1, 11.5, ZB chapter 6.6,15.1,16.1-16.5,17.1, SK video
TI: Felsenstein algorithm, algorithms for HMM and phyloHMM, HW1 model solutions pdf SK notes
TB: K-means clustering, enrichment, multiple testing correction pdf pdf SK notes
Nov. 18
L: Protein structure and function
DEKM chapter 5; ZB chapter 4.8-4.10, 6.1-6.2, 13.1-13.2, SK video
TI: Motif finding by EM and Gibbs sampling
TB: Introduction to context-free grammars, Uniprot
Nov. 25
L: RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles
DEKM chapter 10, ZB chapter 11.9, SK video
TI: Examples of biological databases, introduction to context-free grammars
TB: Nussinov algorithm
Dec. 2
L: Population genetics
SK video
TI: RNA structure
TB: Microarray data, RNA structure, MEME, transcription factors in SGD, population genetics
Dec. 9
L: No lecture
TI: Course summary, protein threading via integer linear programming
TB: Course summary, graphs, PSI-BLAST, Pfam, genes, comparative genomics, example of command-line tools
Dec. 16
L: Optional journal club presentations