Izazovi i algoritmi u bioinformatici

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Mladen Lazarević
Izazovi i algoritmi u bioinformatici

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Birth of bioinformatics -Human Genome
Project
■ Referentni genom je reprezentativni primer genoma neke vrste
■ Genom svake jedinke vrste se razlikuje od referentnog genoma na nekim
mestima
■ Referentni genom se koristi kao koordinatni sistem za genomske podatke
■ Međunarodna inicijativa da se napravi rerefenti genom za ljudsku vrstu
■ Trajala je od 1990 do 2003, i koštao preko 3B$
■ Problemi - zbog veličine genoma: kako skladištiti, pristupiti i analizirati podatke
-> Bioinformatics

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Bioinformatics vs Data science

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Bioinformatics vs Data science
● Spoj između genomskih podataka i naučnih zaključaka
● (Uglavnom) fokus na jednom semplu umesto na populaciju semplova
● Tražimo specifične motive u genomu - mutacije, eskpresije gena, strukturne varijante
○ 3,000,000,000 karaktera {A, C, G, T}
○ Veliki semplovi: 100 - 400 GB
● Problem se teško apstrahuje
○ Često se vraćamo nazad koja je biološka pozadina problema i kako su podaci generisani

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Sekvenciranje i rekonstrukcija genoma

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Bioinformatics recap (1)
Tipičan sempl (Genom):
● 200-500 miliona readova
● Svaki read ima 50-150 karaktera (A, C, G, T)
● + kvalitet očitavanja
● 30x coverage ~ 150-300GB
Različiti podaci:
● Digitalizovani DNK, RNK, proteini
● Različite tehnike (lab prep)

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Bioinformatics recap (2)
Najčešći početak:
Rekonstrukcija genoma

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Genome assembly

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Genome assembly

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Alignment

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Alignment

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Alignment - suffix array
Query:
O(n log m)~O(n+logm)
Space:
m~3m integers
Build (sort):
O(m2
logm)~O(m2
)~O(m logm)

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Alignment - BWT

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Alignment - BWT
● BWM podseća na suffix array
● Redosled sortiranja je isti bilo da su vrste rotacije ili sufiksi

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Alignment - BWT

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Alignment - BWT
Final data structure:
1. BWT
2. Checkpoints
3. Suffix array

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IZAZOVI BIOINFORMATIKE

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PRIMENA BIOINFORMATIKE

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Personalizovana medicina

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Primer studije personalizovane medicine

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HVALA!