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undergraduate thesis
Poravnanje dugačkih RNA očitanja
2016. urn:nbn:hr:168:586637
Jurić, Antonio
University of Zagreb
Faculty of Electrical Engineering and Computing

Cite this document

Jurić, A. (2016). Poravnanje dugačkih RNA očitanja (Undergraduate thesis). Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing. Retrieved from https://urn.nsk.hr/urn:nbn:hr:168:586637

Jurić, Antonio. "Poravnanje dugačkih RNA očitanja." Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2016. https://urn.nsk.hr/urn:nbn:hr:168:586637

Jurić, Antonio. "Poravnanje dugačkih RNA očitanja." Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2016. https://urn.nsk.hr/urn:nbn:hr:168:586637

Jurić, A. (2016). 'Poravnanje dugačkih RNA očitanja', Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, accessed 20 April 2024, https://urn.nsk.hr/urn:nbn:hr:168:586637

Jurić A. Poravnanje dugačkih RNA očitanja [Undergraduate thesis]. Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing; 2016 [cited 2024 April 20] Available at: https://urn.nsk.hr/urn:nbn:hr:168:586637

A. Jurić, "Poravnanje dugačkih RNA očitanja", Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb, 2016. Available at: https://urn.nsk.hr/urn:nbn:hr:168:586637

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Metadata
TitlePoravnanje dugačkih RNA očitanja
Title (english)RNA-seq aligner for long reads
AuthorAntonio Jurić
MentorMile Šikić (mentor)
Committee memberMile Šikić (predsjednik povjerenstva)
Committee memberKrešimir Križanović (član povjerenstva)
Committee memberRobert Vaser (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Electrical Engineering and Computing
Zagreb
Defense date and country2016-09-12, Croatia
Scientific / art field,
discipline and subdiscipline		TECHNICAL SCIENCES
Computing
Abstract
Poravnanje dugačkih RNA očitanja jest problem pronalska s kojeg dijela reference je nastalo dobiveno RNA očitanje. Problem se razlikuje od poravnanja DNA nizova u kojem želimo sastaviti cjelokupni genom zbog posebnih stvojstava RNA koja bitno kompliciraju cijeli proces. U ovom radu opisana je problematika poravnanja nizova RNA. Alat za poravnanje nizova GraphMap problem poravnanja nizova RNA rješava u pet faza: posljednju fazu obrađuje ovaj rad. U toj fazi pokušavamo pronaći najbolje grupe (manje dijelove očitanja) za poravnanje pojedinog očitanja. Algoritam koji je razvijen za problem odabira najboljih grupa sadrži dva algoritma koji se pokreću ovisno u ukupnom broju grupa: knapsack složenosti 𝑂(𝑁^2) te 2D logaritamsku strukturu složenosti 𝑂(𝑁⋅𝑙𝑜𝑔^2(𝑁)) gdje je N broj grupa.
Abstract (english)
Long RNA-seq alignment is problem of finding from which part of reference RNA read comes from. Problem is different from DNA alignment in which we want to compose whole genome because of special properties of RNA which make whole process more complicated. In this paper process of RNA alignment is described. Tool for alignment GraphMap solves the problem of alignment in five phases: last phase is described in this paper. In that phase we try to find best clusters (smaller parts of reads) for alignment of one read. Algorithm which is developed for problem of selecting best clusters is composed of two algorithms which are used depending on total number of clusters: knapsack with complexity of 𝑂(𝑁^2) and 2D logarithmic structure with complexity of 𝑂(𝑁⋅𝑙𝑜𝑔^2(𝑁)) where N is the number of clusters.
Keywords
Keywords (english)
Languagecroatian
URN:NBNurn:nbn:hr:168:586637
Study programmeTitle: Computing
Study programme type: university
Study level: undergraduate
Academic / professional title: sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva (sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva)
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Created on2018-02-06 09:30:45