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undergraduate thesis
Mapiranje kratkih očitanja
Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing, 2019. urn:nbn:hr:168:286362
Pavlić, Stanislav
University of Zagreb
Faculty of Electrical Engineering and Computing

Institutional repository: FER Repository

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Pavlić, S. (2019). Mapiranje kratkih očitanja (Undergraduate thesis). Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing. Retrieved from https://urn.nsk.hr/urn:nbn:hr:168:286362

Pavlić, Stanislav. "Mapiranje kratkih očitanja." Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2019. https://urn.nsk.hr/urn:nbn:hr:168:286362

Pavlić, Stanislav. "Mapiranje kratkih očitanja." Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2019. https://urn.nsk.hr/urn:nbn:hr:168:286362

Pavlić, S. (2019). 'Mapiranje kratkih očitanja', Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, accessed 06 August 2024, https://urn.nsk.hr/urn:nbn:hr:168:286362

Pavlić S. Mapiranje kratkih očitanja [Undergraduate thesis]. Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing; 2019 [cited 2024 August 06] Available at: https://urn.nsk.hr/urn:nbn:hr:168:286362

S. Pavlić, "Mapiranje kratkih očitanja", Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb, 2019. Available at: https://urn.nsk.hr/urn:nbn:hr:168:286362

Metadata
TitleMapiranje kratkih očitanja
Title (english)Short Reads Mapping
AuthorStanislav Pavlić
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 country2019-07-12, Croatia
Scientific / art field,
discipline and subdiscipline		TECHNICAL SCIENCES
Computing
Abstract
Kratka očitanja se većinom koriste u slučaju kada imamo već poznati, referentni genom neke vrste ili referencu, i želimo utvrditi razlike između reference i pojedine jedinke koju sekvenciramo. U ovom radu razvijena je metoda mapiranja kratkih očitanja na referencu koja je podijeljena na dvije faze. Prva faza sastoji se od indeksiranja kratkih podnizova na referenci i pronalaska kandidatnih pozicija pomoću zajedničkih podnizova na referenci i očitanjima te algoritma za traženje najdulje zajedničke podsekvence. U drugoj fazi koristi se KSW2 algoritam za određivanje optimalnog poravnanja dva niza. Provedeno je ispitivanje rješenja na stvarnim podatcima koje je pokazalo da bi se uz određena poboljšanja metoda mogla mjeriti s trenutno korištenim metodama. Implementacija je napisana u jeziku C/C++, a izvorni kod dostupan je na https://github.com/lbcb-edu/BSc-thesis-18-19/tree/spavlic.
Abstract (english)
Short reads are mostly used when we already have a known reference genome of a species, and we want to determine the differences between the reference and the individual being sequenced. In this thesis, a method for mapping short reads consisting of two phases was developed. The first phase includes indexing short substrings of the reference and finding candidate positions using substrings that are in common to the reference and the read, with the help of the longest common subsequence algorithm. In the second phase the KSW2 algorithm is used for determining the optimal alignment of the two sequences. The solution was tested on a real-world dataset which showed that with some improvements, the method might be able to rival the methods that are currently in use. The implementation was written in C/C++ and the source code is available at https://github.com/lbcb-edu/BSc-thesis-18-19/tree/spavlic.
Keywords
Keywords (english)
Languagecroatian
URN:NBNurn:nbn:hr:168:286362
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)
Type of resourceText
File originBorn digital
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Created on2020-01-07 21:05:58