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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Riadok 33: Riadok 33:
 
{{T|Sept. 22||1}}
 
{{T|Sept. 22||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 SK video 1] [https://www.youtube.com/watch?v=iHt5WPVFd7E SK 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]
{{R | TI| Introduction to biology  | {{pdf|ci-introbio}} | [[CI01|SK notes]] }}
+
{{R | TI| Introduction to biology  | {{pdf|ci-introbio}} | [[CI01|notes]] }}
{{Lit2 | ZB chapter 1}}, [https://www.youtube.com/watch?v=EtPqUOHTJD4 SK video]
+
{{Lit2 | ZB chapter 1}}, [https://www.youtube.com/watch?v=EtPqUOHTJD4 video]
{{R | TB| Introduction to computer science, UCSC genome browser | {{pdf|cb-introcs}} |  [[CB01|SK notes]] }}
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{{R | TB| Introduction to computer science, UCSC genome browser | {{pdf|cb-introcs}} |  [[CB01|notes]] }}
 
|-
 
|-
 
{{T|Sept. 29||2}}
 
{{T|Sept. 29||2}}
 
{{R | L| Genome assembly 2 | {{pdf|p-seq2}} | }}
 
{{R | L| Genome assembly 2 | {{pdf|p-seq2}} | }}
{{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg SK video]
+
{{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg video]
{{R | TI| Introduction to probability, genome coverage by sequencing reads | {{pdf|ci-coverage}} (SK) | [[CI02|SK notes]] }}
+
{{R | TI| Introduction to probability, genome coverage by sequencing reads | {{pdf|ci-coverage}} | [[CI02|notes]] }}
{{R | TB| Introduction to dynamic programming, introduction to probability | {{pdf|cb-dp}} |  [[CB02|SK notes]] }}
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{{R | TB| Introduction to dynamic programming, introduction to probability | {{pdf|cb-dp}} |  [[CB02|notes]] }}
 
|-
 
|-
 
{{T|Oct. 6||3}}  
 
{{T|Oct. 6||3}}  
 
{{R | L| Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring |  {{pdf|p-aln1}} | }}
 
{{R | L| Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring |  {{pdf|p-aln1}} | }}
{{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 SK video]
+
{{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}} (SK) | [[CI03|SK notes]] }}
+
{{R | TI|Introduction to dynamic programming, proteomics | {{pdf|ci-msms}} | [[CI03|notes]] }}
{{R | TB|Dynamic programming for sequence alignment, dotplots | {{pdf|cb-dotplots}} | [[CB03|SK notes]] }}
+
{{R | TB|Dynamic programming for sequence alignment, dotplots | {{pdf|cb-dotplots}} | [[CB03|notes]] }}
 
|-
 
|-
 
{{T|Oct. 13||4}}
 
{{T|Oct. 13||4}}
 
{{R | L| Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments | {{pdf|p-aln2}} | }}
 
{{R | L| Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments | {{pdf|p-aln2}} | }}
{{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 SK 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|SK notes]] }}
+
{{R | TI|Advanced algorithms for sequence alignment | |  [[CI04|notes]] }}
{{R | TB|Programs for sequence alignment, scoring schemes| | [[CB04|SK notes]] }}
+
{{R | TB|Programs for sequence alignment, scoring schemes| | [[CB04|notes]] }}
 
|-
 
|-
 
{{T|Oct. 20||5}}
 
{{T|Oct. 20||5}}
{{R | L| Gene finding, hidden Markov models | <!-- {{pdf|p-gene-en}} --> | }}
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{{R | L| Gene finding, hidden Markov models | {{pdf|p-gene}}| }}
{{Lit2 | BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7}}, [https://www.youtube.com/watch?v=jkQGXiqKbxM SK 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 | | <!-- [[CI05|SK notes]] --> }}
+
{{R | TI|Fast similarity search, BLAST, MinHash | {{pdf|ci-seeds}} | [[CI05|notes]] }}
{{R | TB|Hidden Markov models, E-value |  <!-- {{pdf|cb-evalue}} --> | <!-- [[CB05|SK notes]] --> }}
+
{{R | TB|Hidden Markov models, E-value |  {{pdf|cb-evalue}} | [[CB05|notes]] }}
 
|-
 
|-
 
{{T|Oct. 27||6}}
 
{{T|Oct. 27||6}}
{{R | L| Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | <!-- {{pdf|p-phylo-en}} --> | }}
+
{{R | L| Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | {{pdf|p-phylo}} | }}
{{Lit2 | BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2}}, [https://youtu.be/RzfNHvZH4l8 SK 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-en}} --> | <!-- [[CI06|SK notes]] --> }}
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{{R | TI|Algorithms for HMM | {{pdf|ci-hmm}}  | [[CI06|notes]] }}
{{R | TB|Substitution models, bootstrap, tree rooting| <!-- {{pdf|cb-phylo}} --> | <!-- [[CB06|SK notes]] --> }}
+
{{R | TB|Substitution models, bootstrap, tree rooting| {{pdf|cb-phylo}} | [[CB06|notes]] }}
 
|-
 
|-
 
{{T|Nov. 3||7}}
 
{{T|Nov. 3||7}}
{{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs |  <!-- {{pdf|p-compgen-en}} --> | }}
+
{{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs |  {{pdf|p-compgen}} | }}
{{Lit2 | BV chapter 5, ZB chapter 9.8, 10.8}}, [https://youtu.be/1WM4QI2qx8A SK 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|SK notes]] --> }}
+
{{R | TI|Substitution models |  {{pdf|ci-matice-en}} | [[CI07|notes]] }}
{{R | TB|Phylogenetic trees |  | <!-- [[CB07|SK notes]] --> }}
+
{{R | TB|Phylogenetic trees |  | [[CB07|notes]] }}
 
|-
 
|-
 
{{T|Nov. 10||8}}
 
{{T|Nov. 10||8}}
{{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | <!-- {{pdf|p-expr-en}} --> | }}
+
{{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | {{pdf|p-expr}} | }}
 
{{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|SK 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|SK notes]] -->}}
+
{{R | TB|K-means clustering, enrichment, multiple testing correction| {{pdf|cb-kmeans}} {{pdf|cb-enrichment-en}} | [[CB08|notes]]}}
 
|-
 
|-
 
{{T|Nov. 17|No lecture, no tutorials|}}
 
{{T|Nov. 17|No lecture, no tutorials|}}
 
|-
 
|-
 
{{T|Nov. 24||10}}
 
{{T|Nov. 24||10}}
{{R | L| Protein structure and function |  <!-- {{pdf|p-prot-en}} --> | }}
+
{{R | L| Protein structure and function |  {{pdf|p-prot}} | }}
 
{{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|SK notes]] --> }}
+
{{R | TI|Motif finding by EM and Gibbs sampling |  |  [[CI09|notes]] }}
{{R | TB|Introduction to context-free grammars | | <!-- [[CB09|SK notes]] --> }}
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{{R | TB|Introduction to context-free grammars | | [[CB09|notes]] }}
 
|-
 
|-
 
{{T|Dec. 1||11}}
 
{{T|Dec. 1||11}}
{{R | L| RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles | <!-- {{pdf|p-rna-en}} --> | }}
+
{{R | L| RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles | {{pdf|p-rna}} | }}
 
{{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 |  <!-- {{pdf|cb-compgen}}, {{pdf|cb-gene}} --> | <!-- [[CI10|SK notes]] --> |  }}
+
{{R | TI| Examples of biological databases, HW1 model solutions, introduction to context-free grammars |  | [[CI10|notes]] |  }}
{{R | TB| Genes, comparative genomics, Pfam  | | <!-- [[CB10|SK notes]] --> }}
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{{R | TB| Genes, comparative genomics, Pfam  | | [[CB10|notes]] }}
 
|-
 
|-
 
{{T|Dec. 8||12}}
 
{{T|Dec. 8||12}}
{{R | L| Population genetics | <!-- {{pdf|p-popgen-en}} --> | }}
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{{R | L| Population genetics | {{pdf|p-popgen}} | }}
 
{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
 
{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
{{R | TI| RNA structure  |  | <!-- [[CI11|SK notes]] --> }}
+
{{R | TI| RNA structure  |  | [[CI11|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}} --> | <!-- [[CB11|SK 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}}  | [[CB11|notes]]  }}
 
|-
 
|-
 
{{T|Dec. 15||13}}
 
{{T|Dec. 15||13}}
 
{{R | L| Optional journal club presentations | | }}
 
{{R | L| Optional journal club presentations | | }}
{{R | TI| Course summary, protein threading via integer linear programming | <!-- {{pdf|ci-summary-en}}, {{pdf|ci-ilp-en}} --> | <!-- [[CI12|SK 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| Cancelled <!-- example of command-line tools--> | <!--{{pdf|cb-summary}}, {{pdf|cb-graphs}}--> | <!--[[CB12|notes]]--> }}
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{{R | TB| Example of command-line tools | <!--{{pdf|cb-summary}}, {{pdf|cb-graphs}}--> | <!--[[CB12|notes]]--> }}
 
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Verzia zo dňa a času 13:53, 8. december 2022

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. 22
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. 29
L: Genome assembly 2 pdf
video
TI: Introduction to probability, genome coverage by sequencing reads pdf notes
TB: Introduction to dynamic programming, introduction to probability pdf notes
Oct. 6
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, video
TI: Introduction to dynamic programming, proteomics pdf notes
TB: Dynamic programming for sequence alignment, dotplots pdf notes
Oct. 13
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, video
TI: Advanced algorithms for sequence alignment notes
TB: Programs for sequence alignment, scoring schemes notes
Oct. 20
L: Gene finding, hidden Markov models pdf
BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7, video
TI: Fast similarity search, BLAST, MinHash pdf notes
TB: Hidden Markov models, E-value pdf notes
Oct. 27
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, video
TI: Algorithms for HMM pdf notes
TB: Substitution models, bootstrap, tree rooting pdf notes
Nov. 3
L: Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs pdf
BV chapter 5, ZB chapter 9.8, 10.8, video
TI: Substitution models pdf notes
TB: Phylogenetic trees notes
Nov. 10
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 pdf notes
TB: K-means clustering, enrichment, multiple testing correction pdf pdf notes
Nov. 17 No lecture, no tutorials
Nov. 24
L: Protein structure and function pdf
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 notes
TB: Introduction to context-free grammars notes
Dec. 1
L: RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles pdf
DEKM chapter 10, ZB chapter 11.9, SK video
TI: Examples of biological databases, HW1 model solutions, introduction to context-free grammars notes
TB: Genes, comparative genomics, Pfam notes
Dec. 8
L: Population genetics pdf
SK video
TI: RNA structure notes
TB: PSI-BLAST, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics, course summary, graphs pdf, pdf notes
Dec. 15
L: Optional journal club presentations
TI: Course summary, protein threading via integer linear programming
TB: Example of command-line tools