1-BIN-301, 2-AIN-501 Methods in Bioinformatics, 2021/22

Introduction · Rules · Tasks and dates · Materials · Moodle · Discussion
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.


Materials: Rozdiel medzi revíziami

Z MBI
Prejsť na: navigácia, hľadanie
(29 intermediate revisions by the same user not shown)
Riadok 7: Riadok 7:
 
* '''ZB''': Zvelebil, Baum: Understanding Bioinformatics. Taylor & Francis 2008. Can be studied in the FMFI  library under code I-INF-Z-2
 
* '''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.  
+
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'''
 
'''Recordings of lectures in Slovak from 2018/19'''
* [https://www.youtube.com/playlist?list=PLU2XVjShDFwVeTDmo9Uv2NHWz3ijUjy5p playlist na youtube]
+
* [https://www.youtube.com/playlist?list=PLU2XVjShDFwVeTDmo9Uv2NHWz3ijUjy5p playlist on youtube]
  
  
Riadok 20: Riadok 20:
 
<!--
 
<!--
 
Pouzitie sablon:
 
Pouzitie sablon:
tyzden: {{T|datumy od-do|nepovinny dalsi text}}
+
tyzden: {{T|datumy od-do|nepovinny dalsi text|cislo tyzdna}}
 
riadok (hodina): {{R| aka hodina, t.j. L alebo TI alebo TB| popis | {{pdf|meno pdf suboru}} | [[wiki poznamky|poznamky]] }}
 
riadok (hodina): {{R| aka hodina, t.j. L alebo TI alebo TB| popis | {{pdf|meno pdf suboru}} | [[wiki poznamky|poznamky]] }}
 
literatura: {{Lit | cisla kapitol}}
 
literatura: {{Lit | cisla kapitol}}
Riadok 27: Riadok 27:
 
-->
 
-->
  
[[#w3]], [[#w3b]]
+
{{W|1}}, {{W|2}}, {{W|3}}, {{W|4}}, {{W|5}}, {{W|6}}, {{W|7}}, {{W|8}}, {{W|9}}, {{W|10}}, {{W|11}}, {{W|12}}, {{W|13}}
  
 
{|
 
{|
 
|-
 
|-
{{T|Sept. 23|}}
+
{{T|Sept. 23||1}}
 
{{R | L| Introduction, course rules, sequencing and genome assembly | {{pdf|p-intro-en}}, {{pdf|p-seq-en}} | }}
 
{{R | L| Introduction, course rules, sequencing and genome assembly | {{pdf|p-intro-en}}, {{pdf|p-seq-en}} | }}
 
{{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 SK video 1] [https://www.youtube.com/watch?v=iHt5WPVFd7E SK video 2]
Riadok 44: Riadok 44:
 
{{R | TB| Introduction to dynamic programming, introduction to probability | {{pdf|cb-dp}} |  [[CB02|SK notes]] }}
 
{{R | TB| Introduction to dynamic programming, introduction to probability | {{pdf|cb-dp}} |  [[CB02|SK notes]] }}
 
|-
 
|-
{{T|Oct. 7||3}} <span id="w3b">x</span>y
+
{{T|Oct. 7||3}}  
|-
+
| <span id="w3">x</span>y
+
|-
+
 
{{R | L| Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring |  {{pdf|p-aln1-en}} | }}
 
{{R | L| Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring |  {{pdf|p-aln1-en}} | }}
 
{{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 SK video]
Riadok 53: Riadok 50:
 
{{R | TB|Dynamic programming for sequence alignment, dotplots | {{pdf|cb-dotplots}} |  [[CB03|notes]] }}
 
{{R | TB|Dynamic programming for sequence alignment, dotplots | {{pdf|cb-dotplots}} |  [[CB03|notes]] }}
 
|-
 
|-
{{T|Oct. 14|}}
+
{{T|Oct. 14||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-en}} | }}
 
{{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 SK video]
 
{{R | TI|Advanced algorithms for sequence alignment | |  [[CI04|SK notes]] }}
 
{{R | TI|Advanced algorithms for sequence alignment | |  [[CI04|SK notes]] }}
{{R | TB|Programs for sequence alignment, scoring schemes| | <!-- [[CB04|notes]]--> }}
+
{{R | TB|Programs for sequence alignment, scoring schemes| | [[CB04|SK notes]] }}
 
|-
 
|-
{{T|Oct. 21|}}
+
{{T|Oct. 21||5}}
{{R | L| Gene finding, hidden Markov models | <!--{{pdf|p-gene}}--> | }}
+
{{R | L| Gene finding, hidden Markov models | {{pdf|p-gene-en}} | }}
 
{{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 SK video]
{{R | TI|Fast similarity search, BLAST, MinHash |  | <!--[[CI05|notes]]--> }}
+
{{R | TI|Fast similarity search, BLAST, MinHash |  | [[CI05|SK notes]] }}
{{R | TB|Hidden Markov models, E-value |  | <!--[[CB05|notes]]--> }}
+
{{R | TB|Hidden Markov models, E-value |  {{pdf|cb-evalue}} | [[CB05|SK notes]] }}
 
|-
 
|-
{{T|Oct. 28|}}
+
{{T|Oct. 28||6}}
{{R | L| Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | <!--{{pdf|p-phylo}}--> | }}
+
{{R | L| Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | {{pdf|p-phylo-en}} | }}
 
{{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 SK video]
{{R | TI|Algorithms for HMM | <!-- {{pdf|ci-hmm}} --> | <!--[[CI06|notes]]--> }}
+
{{R | TI|Algorithms for HMM | {{pdf|ci-hmm-en}}  | [[CI06|SK notes]] }}
{{R | TB|Substitution models, bootstrap, tree rooting, Fitch's algorithm| <!-- {{pdf|cb-phylo}} --> <!--{{pdf|cb-phylo-en}}--> | <!--[[CB06|notes]]--> }}
+
{{R | TB|Substitution models, bootstrap, tree rooting| {{pdf|cb-phylo}} <!--{{pdf|cb-phylo-en}}--> | [[CB06|SK notes]] }}
 
|-
 
|-
{{T|Nov. 4|}}
+
{{T|Nov. 4||7}}
{{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs |  <!--{{pdf|p-compgen}}-->  | }}
+
{{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs |  {{pdf|p-compgen-en}} | }}
 
{{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 SK video]
{{R | TI|Substitution models |  <!-- {{pdf|ci-matice}} --> <!--[[CI07|notes]]--> }}
+
{{R | TI|Substitution models |  {{pdf|ci-matice-en}} |  [[CI07|SK notes]] }}
{{R | TB|E-value, phylogenetic trees | <!--{{pdf|cb-evalue}}--> <!-- {{pdf|cb-compgen}}, {{pdf|cb-gene}}--> | <!--[[CB07|notes]]--> }}
+
{{R | TB|Phylogenetic trees | | [[CB07|SK notes]] }}
 
|-
 
|-
{{T|Nov. 11|}}
+
{{T|Nov. 11||8}}
{{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | <!--{{pdf|p-expr}}--> | }}
+
{{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | {{pdf|p-expr-en}} | }}
 
{{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, HW1 model solutions | <!-- {{pdf|ci-hmm}} --> | <!--[[CI08|notes]]--> }}
+
{{R | TI|Felsenstein algorithm, algorithms for HMM and phyloHMM | {{pdf|ci-hmm}} | [[CI08|SK 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|SK notes]] }}
 
|-
 
|-
{{T|Nov. 18|}}
+
{{T|Nov. 18||9}}
{{R | L| Protein structure and function |  <!--{{pdf|p-prot}}--> | }}
+
{{R | L| Protein structure and function |  {{pdf|p-prot-en}} | }}
 
{{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|SK notes]] }}
{{R | TB|Introduction to context-free grammars, Uniprot | | <!--[[CB09|notes]]--> }}
+
{{R | TB|Introduction to context-free grammars | | [[CB09|SK notes]] }}
 
|-
 
|-
{{T|Nov. 25|}}
+
{{T|Nov. 25||10}}
{{R | L| RNA, sekundárna štruktúra, Nussinovovej algoritmus, stochastické bezkontextové gramatiky, profily RNA rodín | <!--{{pdf|p-rna}}--> | }}
+
{{R | L| RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles | {{pdf|p-rna-en}} | }}
 
{{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| Ukážky biologických databáz, úvod do bezkontextových gramatík |  | <!--[[CI10|notes]]--> |  }}
+
{{R | TI| Examples of biological databases, HW1 model solutions, introduction to context-free grammars {{pdf|cb-compgen}}, {{pdf|cb-gene}} | [[CI10|SK notes]] |  }}
{{R | TB| Nussinovovej algoritmus | | <!--[[CB10|notes]]--> }}
+
{{R | TB| Genes, comparative genomics, Pfam  | | [[CB10|SK notes]] }}
 
|-
 
|-
{{T|Dec. 2|}}
+
{{T|Dec. 2||11}}
{{R | L| Populačná genetika | <!--{{pdf|p-popgen}}--> | }}
+
{{R | L| No lecture, no tutorials | | }}
{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
+
{{R | TI| RNA štruktúra  |  | <!--[[CI11|notes]]--> }}
+
{{R | TB| Microarray dáta, RNA štruktúra, MEME, transkripčné faktory v SGD, populačná genetika | | <!--[[CB11|notes]]-->  }}
+
 
|-
 
|-
{{T|Dec. 9|}}
+
{{T|Dec. 9||12}}
{{R | L| Prednáška nebude | | }}
+
{{R | L| Population genetics | {{pdf|p-popgen-en}} | }}
{{R | TI| Zhrnutie semestra, Protein threading pomocou celočíselného lineárneho programovania | <!--{{pdf|ci-summary}}, {{pdf|ci-ilp}}--> | <!--[[CI12|notes]]--> }}
+
{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
{{R | TB| Zhrnutie semestra, grafy, PSI-BLAST, Pfam, gény, komparatívna genomika, ukážka práce na príkazovom riadku | <!--{{pdf|cb-summary}}, {{pdf|cb-graphs}}--> | <!--[[CB12|notes]]--> }}
+
{{R | TI| RNA structure  |  | [[CI11|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|SK notes]] }}
 
|-
 
|-
{{T|Dec. 16|}}
+
{{T|Dec. 16||13}}
{{R | L| Nepovinné prezentácie | | }}
+
{{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]] }}
 +
{{R | TB| Cancelled <!-- example of command-line tools--> | <!--{{pdf|cb-summary}}, {{pdf|cb-graphs}}--> | <!--[[CB12|notes]]--> }}
 
|-
 
|-
 
|}
 
|}

Verzia zo dňa a času 10:55, 16. december 2021

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. 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 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 pdf SK notes
TB: K-means clustering, enrichment, multiple testing correction pdf pdf SK notes
Nov. 18
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 SK notes
TB: Introduction to context-free grammars SK notes
Nov. 25
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 pdf, pdf SK notes
TB: Genes, comparative genomics, Pfam SK notes
Dec. 2
L: No lecture, no tutorials
Dec. 9
L: Population genetics pdf
SK video
TI: RNA structure SK notes
TB: PSI-BLAST, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics, course summary, graphs pdf, pdf SK notes
Dec. 16
L: Optional journal club presentations
TI: Course summary, protein threading via integer linear programming pdf, pdf SK notes
TB: Cancelled