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.


Materials: Rozdiel medzi revíziami

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Riadok 31: Riadok 31:
 
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{{T|Sept. 22||1}}
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{{T|Sept. 21||1}}
 
{{R | L| Introduction, course rules, sequencing and genome assembly |  {{pdf|p-intro}}, {{pdf|p-seq}} | }}
 
{{R | L| Introduction, course rules, sequencing and genome assembly |  {{pdf|p-intro}}, {{pdf|p-seq}} | }}
 
{{Lit2 | BV chapter 1}}, [https://www.youtube.com/watch?v=3HI-wKmTuSs video 1] [https://www.youtube.com/watch?v=iHt5WPVFd7E video 2]
 
{{Lit2 | BV chapter 1}}, [https://www.youtube.com/watch?v=3HI-wKmTuSs video 1] [https://www.youtube.com/watch?v=iHt5WPVFd7E video 2]
Riadok 38: Riadok 38:
 
{{R | TB| Introduction to computer science, UCSC genome browser | {{pdf|cb-introcs}} |  [[CB01|notes]] }}
 
{{R | TB| Introduction to computer science, UCSC genome browser | {{pdf|cb-introcs}} |  [[CB01|notes]] }}
 
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{{T|Sept. 29||2}}
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{{T|Sept. 28||2}}
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{{R | L| Genome assembly 2 | {{pdf|p-seq2}} | }}
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{{R | L| Genome assembly 2 | <!-- {{pdf|p-seq2}} --> | }}
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{{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg video]
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<!-- {{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg video]  
 
{{R | TI| Introduction to probability, genome coverage by sequencing reads | {{pdf|ci-coverage}} | [[CI02|notes]] }}
 
{{R | TI| Introduction to probability, genome coverage by sequencing reads | {{pdf|ci-coverage}} | [[CI02|notes]] }}
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{{R | TB| Introduction to dynamic programming, introduction to probability | {{pdf|cb-dp}} | [[CB02|notes]] }}
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{{R | TB| Introduction to dynamic programming, introduction to probability | {{pdf|cb-dp}} | [[CB02|notes]] }} -->
 
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{{T|Oct. 6||3}}  
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{{T|Oct. 5||3}}  
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{{R | L| Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring |  {{pdf|p-aln1}} | }}
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{{R | L| Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring |  <!-- {{pdf|p-aln1}} -->| }}
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{{Lit2 | BV chapter 2, DEKM chapter 2.1-2.4, 2.8, ZB chapter 4.1-4.4, 5.1-5.2}}, [https://www.youtube.com/watch?v=0GkhkRiqbl4 video]
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<!-- {{Lit2 | BV chapter 2, DEKM chapter 2.1-2.4, 2.8, ZB chapter 4.1-4.4, 5.1-5.2}}, [https://www.youtube.com/watch?v=0GkhkRiqbl4 video]  
 
{{R | TI|Introduction to dynamic programming, proteomics | {{pdf|ci-msms}} | [[CI03|notes]] }}
 
{{R | TI|Introduction to dynamic programming, proteomics | {{pdf|ci-msms}} | [[CI03|notes]] }}
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{{R | TB|Dynamic programming for sequence alignment, dotplots | {{pdf|cb-dotplots}} | [[CB03|notes]] }}
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{{R | TB|Dynamic programming for sequence alignment, dotplots | {{pdf|cb-dotplots}} | [[CB03|notes]] }} -->
 
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{{T|Oct. 13||4}}
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{{T|Oct. 12||4}}
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{{R | L| Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments | {{pdf|p-aln2}} | }}
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{{R | L| Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments | <!-- {{pdf|p-aln2}} --> | }}
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{{Lit2 | BV chapter 2, DEKM chapter 2.5, 2.7, 6.1-6.3; ZB chapter 4.5-4.7, 5.3-5.5}}, [https://www.youtube.com/watch?v=jkQGXiqKbxM video]
 
{{Lit2 | BV chapter 2, DEKM chapter 2.5, 2.7, 6.1-6.3; ZB chapter 4.5-4.7, 5.3-5.5}}, [https://www.youtube.com/watch?v=jkQGXiqKbxM video]
 
{{R | TI|Advanced algorithms for sequence alignment | |  [[CI04|notes]] }}
 
{{R | TI|Advanced algorithms for sequence alignment | |  [[CI04|notes]] }}
 
{{R | TB|Programs for sequence alignment, scoring schemes| | [[CB04|notes]] }}
 
{{R | TB|Programs for sequence alignment, scoring schemes| | [[CB04|notes]] }}
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{{T|Oct. 20||5}}
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{{T|Oct. 19||5}}
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{{R | L| Gene finding, hidden Markov models | {{pdf|p-gene}}| }}
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{{R | L| Gene finding, hidden Markov models | <!-- {{pdf|p-gene}} -->| }}
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{{Lit2 | BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7}}, [https://www.youtube.com/watch?v=jkQGXiqKbxM video]
 
{{Lit2 | BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7}}, [https://www.youtube.com/watch?v=jkQGXiqKbxM video]
 
{{R | TI|Fast similarity search, BLAST, MinHash | {{pdf|ci-seeds}} | [[CI05|notes]] }}
 
{{R | TI|Fast similarity search, BLAST, MinHash | {{pdf|ci-seeds}} | [[CI05|notes]] }}
 
{{R | TB|Hidden Markov models, E-value |  {{pdf|cb-evalue}} | [[CB05|notes]] }}
 
{{R | TB|Hidden Markov models, E-value |  {{pdf|cb-evalue}} | [[CB05|notes]] }}
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{{T|Oct. 27||6}}
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{{T|Oct. 26||6}}
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{{R | L| Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | {{pdf|p-phylo}} | }}
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{{R | L| Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | <!-- {{pdf|p-phylo}} --> | }}
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{{Lit2 | BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2}}, [https://youtu.be/RzfNHvZH4l8 video]
 
{{Lit2 | BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2}}, [https://youtu.be/RzfNHvZH4l8 video]
 
{{R | TI|Algorithms for HMM | {{pdf|ci-hmm}}  | [[CI06|notes]] }}
 
{{R | TI|Algorithms for HMM | {{pdf|ci-hmm}}  | [[CI06|notes]] }}
 
{{R | TB|Substitution models, bootstrap, tree rooting| {{pdf|cb-phylo}} | [[CB06|notes]] }}
 
{{R | TB|Substitution models, bootstrap, tree rooting| {{pdf|cb-phylo}} | [[CB06|notes]] }}
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{{T|Nov. 3||7}}
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{{T|Nov. 2||7}}
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{{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs |  {{pdf|p-compgen}} | }}
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{{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs |  <!-- {{pdf|p-compgen}} --> | }}
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{{Lit2 | BV chapter 5, ZB chapter 9.8, 10.8}}, [https://youtu.be/1WM4QI2qx8A video]
 
{{Lit2 | BV chapter 5, ZB chapter 9.8, 10.8}}, [https://youtu.be/1WM4QI2qx8A video]
 
{{R | TI|Substitution models |  {{pdf|ci-matice-en}} | [[CI07|notes]] }}
 
{{R | TI|Substitution models |  {{pdf|ci-matice-en}} | [[CI07|notes]] }}
 
{{R | TB|Phylogenetic trees |  | [[CB07|notes]] }}
 
{{R | TB|Phylogenetic trees |  | [[CB07|notes]] }}
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{{T|Nov. 10||8}}
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{{T|Nov. 9||8}}
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{{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | {{pdf|p-expr}} | }}
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{{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | <!-- {{pdf|p-expr}} -->| }}
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{{Lit2 | DEKM chapter 5.1, 11.5, ZB chapter 6.6,15.1,16.1-16.5,17.1}}, [https://youtu.be/GFJ_oDV1KGU SK video]
 
{{Lit2 | DEKM chapter 5.1, 11.5, ZB chapter 6.6,15.1,16.1-16.5,17.1}}, [https://youtu.be/GFJ_oDV1KGU SK video]
 
{{R | TI|Felsenstein algorithm, algorithms for HMM and phyloHMM | {{pdf|ci-hmm}} | [[CI08|notes]] }}
 
{{R | TI|Felsenstein algorithm, algorithms for HMM and phyloHMM | {{pdf|ci-hmm}} | [[CI08|notes]] }}
 
{{R | TB|K-means clustering, enrichment, multiple testing correction| {{pdf|cb-kmeans}} {{pdf|cb-enrichment-en}} | [[CB08|notes]]}}
 
{{R | TB|K-means clustering, enrichment, multiple testing correction| {{pdf|cb-kmeans}} {{pdf|cb-enrichment-en}} | [[CB08|notes]]}}
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{{T|Nov. 17|No lecture, no tutorials|}}
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{{T|Nov. 16|No lecture, no tutorials|}}
 
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{{T|Nov. 24||10}}
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{{T|Nov. 23||10}}
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{{R | L| Protein structure and function |  {{pdf|p-prot}} | }}
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{{R | L| Protein structure and function |  <!-- {{pdf|p-prot}} --> | }}
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{{Lit2 | DEKM chapter 5; ZB chapter 4.8-4.10, 6.1-6.2, 13.1-13.2}}, [https://youtu.be/ugMM81jZRpc SK video]
 
{{Lit2 | DEKM chapter 5; ZB chapter 4.8-4.10, 6.1-6.2, 13.1-13.2}}, [https://youtu.be/ugMM81jZRpc SK video]
 
{{R | TI|Motif finding by EM and Gibbs sampling |  |  [[CI09|notes]] }}
 
{{R | TI|Motif finding by EM and Gibbs sampling |  |  [[CI09|notes]] }}
 
{{R | TB|Introduction to context-free grammars | | [[CB09|notes]] }}
 
{{R | TB|Introduction to context-free grammars | | [[CB09|notes]] }}
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{{T|Dec. 1||11}}
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{{T|Nov. 30||11}}
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{{R | L| RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles | {{pdf|p-rna}} | }}
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{{R | L| RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles | <!-- {{pdf|p-rna}} --> | }}
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<!--
 
{{Lit2 | DEKM chapter 10, ZB chapter 11.9}}, [https://youtu.be/_Hh03Khsr9k SK video]
 
{{Lit2 | DEKM chapter 10, ZB chapter 11.9}}, [https://youtu.be/_Hh03Khsr9k SK video]
 
{{R | TI| Examples of biological databases, HW1 model solutions, introduction to context-free grammars |  | [[CI10|notes]] |  }}
 
{{R | TI| Examples of biological databases, HW1 model solutions, introduction to context-free grammars |  | [[CI10|notes]] |  }}
 
{{R | TB| Genes, comparative genomics, Pfam  | | [[CB10|notes]] }}
 
{{R | TB| Genes, comparative genomics, Pfam  | | [[CB10|notes]] }}
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{{T|Dec. 8||12}}
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{{T|Dec. 7||12}}
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{{R | L| Population genetics | {{pdf|p-popgen}} | }}
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{{R | L| Population genetics | <!-- {{pdf|p-popgen}} --> | }}
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{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
 
{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
 
{{R | TI| RNA structure  |  | [[CI11|notes]] }}
 
{{R | TI| RNA structure  |  | [[CI11|notes]] }}
 
{{R | TB| Example of command-line tools  |  | [[CB11|notes]]  }}
 
{{R | TB| Example of command-line tools  |  | [[CB11|notes]]  }}
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{{T|Dec. 15||13}}
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{{T|Dec. 14||13}}
 
{{R | L| Optional journal club presentations | | }}
 
{{R | L| Optional journal club presentations | | }}
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{{R | TI| Course summary, protein threading via integer linear programming | <!-- {{pdf|ci-summary-en}}, {{pdf|ci-ilp-en}} --> |  [[CI12|notes]] }}
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{{R | TI| Course summary, protein threading via integer linear programming | {{pdf|ci-summary-en}}, {{pdf|ci-ilp-en}} |  [[CI12|notes]] }}
 
{{R | TB| PSI-BLAST, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics, course summary, graphs | {{pdf|cb-summary}}, {{pdf|cb-graphs}} | [[CB12|notes]] }}
 
{{R | TB| PSI-BLAST, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics, course summary, graphs | {{pdf|cb-summary}}, {{pdf|cb-graphs}} | [[CB12|notes]] }}
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Verzia zo dňa a času 21:50, 18. september 2023

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.

Literature:

  • 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
L: Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs
Nov. 9
L: Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs
Nov. 16 No lecture, no tutorials
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
Zdroj: „http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Materials&oldid=2909“