Algoritmi u poravnavanju očitanja

undergraduate thesis

• Title (english): Algorithms in Read Alignment
• Author: Zorana Vukoša
• Mentor: Goran Igaly (mentor)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2017-07-05, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Poravnanje očitanja je korak u sekvenciranju nove generacije gdje se sva očitanja dobivena s platformi za sekvenciranje uspoređuju s referentnom sekvencom kako bi se dobila željena sekvenca. Razni algoritmi su korišteni kako bi olakšali uređivanje velikih brojeva očitavanja na njihovim točnim pozicijama u odnosu na reference. Algoritmi navedeni u ovom radu su temeljni alati za poravnanje očitanja. Razvoj ideje o ubrzanju i poboljšanju algoritma je prikazan od najosnovnijeg algoritma naivnog uparivanja nizova do offline algoritama koji pretprocesiraju tekst jednom te onda koriste indeks stvoren u toj fazi kako bi pronašli očitanja u fazi pretraživanja. Algoritmi će se unapređivati zajedno s platformama za sekvenciranje te u budućnosti možemo očekivati brže i točnije načine za sekvenciranje željenih genoma.

Abstract (english)

Read alignment is a step in Next generation sequencing where all the reads obtained from sequencing platforms are compared to the reference sequence in order to get the wanted sequence. Various algorithms are used to facilitate ordering of the large number of reads to their exact position in respect to the reference. Algorithms mentioned in this thesis are basis of all the read alignment tools. Evolution of the idea on how to speed up and improve algorithm is shown from the most basic Naive string matching algorithm to offline algorithms that preprocess text once and then use the index created in that phase to match the reads in the searching phase. Algorithms are going to evolve together with the sequencing platforms, so we expect that faster and more accurate ways for sequencing the desired genomes will be found.

• Keywords: poravnanje očitanja; algoritam
• Keywords (english): read alignment; algorithm
• Language: croatian
• URN:NBN: urn:nbn:hr:217:508446
• Study programme: Title: Molecular Biology; Study programme type: university; Study level: undergraduate; Academic / professional title: sveučilišni/a prvostupnik/prvostupnica (baccalaureus/baccalaurea) molekularne biologije (sveučilišni/a prvostupnik/prvostupnica (baccalaureus/baccalaurea) molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2017-09-08 10:11:41