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Samenvatting bio-informatica + oefeningen

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Dit document omvat alle informatie van op de slides en wat er besproken werd in de les. De oplossingen voor de oefeningen die werden gegeven staan er ook mee in (we kregen niet de oplossingen van alle oefeningen).

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  • December 23, 2024
  • 160
  • 2024/2025
  • Summary
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BIOINFORMATICA
INHOUDSOPGAVE

1 – Introductie .............................................................................................................................. 4
Getting started ................................................................................................................................ 4
Expectations ................................................................................................................................... 8
(Not) in this course .......................................................................................................................... 9

2 – Computer science background ............................................................................................... 10
Databases..................................................................................................................................... 10

Algoritmes ..................................................................................................................................... 11
Principes van classificatie .............................................................................................................. 13
Graph theory (graaf theorie)............................................................................................................ 15
Computationele complexiteit ......................................................................................................... 17

Oefeningen ................................................................................................................................... 23

3 – Pairwise alignment ................................................................................................................. 25

Introductie .................................................................................................................................... 25
Dot matrix methode ....................................................................................................................... 31
Global alignment: NW .................................................................................................................... 32
Local alignment: SW ...................................................................................................................... 36

Substitution matrices..................................................................................................................... 40
PAM ........................................................................................................................................... 43
BLOSUM .................................................................................................................................... 47
Oefeningen ................................................................................................................................... 51

4 – Multiple alignment .................................................................................................................. 53
Introductie .................................................................................................................................... 53
Dynamic progamming .................................................................................................................... 56
Progressief .................................................................................................................................... 59

Iteratief ......................................................................................................................................... 62
Consistency-based........................................................................................................................ 64
Phylogeny-aware ........................................................................................................................... 65
Wrap-up ........................................................................................................................................ 65
Oefeningen ................................................................................................................................... 67

5 – Sequence search .................................................................................................................... 68



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, Introductie .................................................................................................................................... 68

Smith-Waterman ........................................................................................................................... 69
FASTA ........................................................................................................................................... 70
BLAST ........................................................................................................................................... 74
Oefeningen ................................................................................................................................... 81

6 – Sequentiepatronen ................................................................................................................. 82
Introductie .................................................................................................................................... 82

Motief representatie ...................................................................................................................... 84
Positiespecifieke scorematrix (PSSM) ......................................................................................... 85
Hidden Markov Model (HMM) ...................................................................................................... 89
Motief discovery ............................................................................................................................ 99

Oefeningen ..................................................................................................................................102

7 – Fylogenie .............................................................................................................................. 105

Introductie ...................................................................................................................................105
Sequentie selctie ..........................................................................................................................111
Multiple alignment ........................................................................................................................112
Substitutiemodellen .....................................................................................................................113

Boom constructie .........................................................................................................................116
Afstandsmethoden................................................................................................................... 119
Karakter-gebaseerde methoden................................................................................................ 125
Boom evaluatie ............................................................................................................................129
Oefeningen ..................................................................................................................................131

8 – Sequence assembly .............................................................................................................. 132

Introductie ...................................................................................................................................132
Sequence assembly theorie ..........................................................................................................132
Oefeningen ..................................................................................................................................139

10 – Mass spectrometry proteomics ........................................................................................... 140
Introductie ...................................................................................................................................140
Een primer voor MS .......................................................................................................................140
Eiwit en peptide MS.......................................................................................................................141
Spectrum identificatie...................................................................................................................145
Sequentie databank search ...................................................................................................... 146
Spectral library search.............................................................................................................. 147
De novo sequencing ................................................................................................................. 147
Statistische overwegingen.............................................................................................................148




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,11 – Netwerk biologie ................................................................................................................. 149

Introductie ...................................................................................................................................149
Moleculair netwerk: types .............................................................................................................150
Moleculair netwerk: eigenschappen ..............................................................................................152
Moleculair netwerk: inferentie .......................................................................................................156
Moleculair netwerk: analyse ..........................................................................................................158
Oefeningen ..................................................................................................................................160




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, 1 – INTRODUCTIE

GETTING STARTED

• Wat kunnen we leren uit sequentie-informatie en hoe doet men dat =
bioinformatica
• Sequentieverschillen moeilijk met blote oog te vinden, moet mbv computer
• Databanken doorzoeken: sequentie vergelijken met wat we ergens in deze
wereld al eerder gezien hebben
• Afleiden van evolutionaire verbanden: relaties tussen verschillende organismen
o Bvb hoe verschillende varianten van virussen zich tov elkaar verhouden
• Ontdekken van frequentiepatronen
o Patronen die regelmatig voorkomen in sequentie
o Stukje sequentie dat in kort stuk DNA verschillende keren voorkomt is
biologisch gezien betekenisvol, kan geen toevam zijn
• Voorspellen eiwitfct
o Verschillende technieken hiervoor
• Menselijk genoom
o Elke cel bevat exacte kopij
o 23 chromosomen
o Complementaire helix
o Enkele streng kan je neerschrijven in
deze vorm: zie afb
• DNA geëxtraheerd uit weefsel (staal organisme) à
kopij maken DNA: amplificatie à in korte
fragmenten knippen à parallel lezen op machine =
sequencer à elk van dotjes (zie afb) is 1 van
fragmentjes, elke kleur is 1 base die ervan gelezen
wordt (dmv excitatie)
o Resultaat: verzameling korte sequenties
o Vergeklijking: 5000 boeken, 30x kopiëren, versnipperen à lezen
• Genome assembly: zoeken naar overlap tussen stukjes à als er overlap is
kunnen het buren zijn, naburige stukjes DNA
o Er kunenn fouten gebeuren, soms onzekerheid
• 2 sequenties: ene gezond, ene ziek à wat onderscheidt gezonde van zieke
individuen
o Voor klein stukje sequentie niet heel moeilijk maar voor heel DNA wel
o Soms kan 1 letter verschil bepalend zijn, maar ziektes zijn vaak complexer
• In 2000 kostte een genoom uitlezen miljarden dollars, nu al technieken van maar
honderden dollars



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