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

Introduction · Rules · Tasks and dates · Materials · Moodle
Cvičenia vo štvrtok o 14:00 sú určené pre študentov BIN, INF, mINF, mAIN, DAV. Cvičenia vo štvrtok o 17:20 sú pre študentov z PriFUK a z fyzikálnych odborov. Obidvoje cvičenia sa budú konať už v prvom týždni semestra.
Quizzes can be found 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. 21
L: Introduction, course rules, sequencing and genome assembly pdf, pdf
BV chapter 1, video 1 video 2
TI: Introduction to biology pdf notes
ZB chapter 1, video
TB: Introduction to computer science, UCSC genome browser pdf notes
Sept. 28
L: Genome assembly 2
Oct. 5
L: Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring
Oct. 12
L: Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments
Oct. 19
L: Gene finding, hidden Markov models
Oct. 26
L: Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution)
Nov. 2 No lecture, no tutorials
Nov. 9
L: Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs
Nov. 16
L: Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs
Nov. 23
L: Protein structure and function
Nov. 30
L: RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles
Dec. 7
L: Population genetics
Dec. 14
L: Optional journal club presentations