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master's thesis
Metoda za mapiranje bisulfitno tretiranih očitanja na genom
Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing, 2022. urn:nbn:hr:168:582319
Kosier, Sanja
University of Zagreb
Faculty of Electrical Engineering and Computing

Institutional repository: FER Repository

Cite this document

Kosier, S. (2022). Metoda za mapiranje bisulfitno tretiranih očitanja na genom (Master's thesis). Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing. Retrieved from https://urn.nsk.hr/urn:nbn:hr:168:582319

Kosier, Sanja. "Metoda za mapiranje bisulfitno tretiranih očitanja na genom." Master's thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2022. https://urn.nsk.hr/urn:nbn:hr:168:582319

Kosier, Sanja. "Metoda za mapiranje bisulfitno tretiranih očitanja na genom." Master's thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2022. https://urn.nsk.hr/urn:nbn:hr:168:582319

Kosier, S. (2022). 'Metoda za mapiranje bisulfitno tretiranih očitanja na genom', Master's thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, accessed 29 August 2024, https://urn.nsk.hr/urn:nbn:hr:168:582319

Kosier S. Metoda za mapiranje bisulfitno tretiranih očitanja na genom [Master's thesis]. Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing; 2022 [cited 2024 August 29] Available at: https://urn.nsk.hr/urn:nbn:hr:168:582319

S. Kosier, "Metoda za mapiranje bisulfitno tretiranih očitanja na genom", Master's thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb, 2022. Available at: https://urn.nsk.hr/urn:nbn:hr:168:582319

Metadata
TitleMetoda za mapiranje bisulfitno tretiranih očitanja na genom
Title (english)Method for Mapping Bisulfite-treated Sequencing Reads To a Genome
AuthorSanja Kosier
MentorMile Šikić (mentor)
Committee memberMile Šikić (predsjednik povjerenstva)
Committee memberMirjana Domazet-Lošo (član povjerenstva)
Committee memberKrešimir Križanović (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Electrical Engineering and Computing
Zagreb
Defense date and country2022-07-01, Croatia
Scientific / art field,
discipline and subdiscipline		TECHNICAL SCIENCES
Computing
Abstract
Bisulfitno sekvenciranje metoda je za detekciju citozinskih modifikacija. Tretman DNA s bisulfitom pretvara citozin u uracil, zadržavajuću 5-metilcitozin nepromijenjen. Umnažanje DNA, koristeći lančanu reakciju polimeraze, rezultira pretvaranjem uracila u timin. Nakon toga DNA se sekvencira. S obzirom da se ne zna kojem lancu pripada pojedino očitanje, mapiranje očitanja koja su bisulfitno tretirana zahtjeva pristup koji uključuje pokretanje četiri procesa mapiranja istovremeno. Cilj ovog diplomskog rada bio je razviti metodu za mapi- ranje bisulfatno tretiranih sekvenci na referetni genom. Budući da je problematika mapiranja bisulfatno tertiranih sekvenci u suštini problematika mapiranja kratkih sekvenci, razvijeni alat u radu se oslanja na novo razvijeni alat za mapiranje Accel-Align. Bisulfitni maper razvijen za potrebe ovog diplomskog rada je javno dostupan na Githubu te je stavljen pod MIT licencu.
Abstract (english)
Bisulfite sequencing is a method for the detection of cytosine methylations. Treatment of DNA with bisulfite converts cytosine to uracil while leaving 5-methylcytosine unchanged. Amplifying DNA material with polymerase chain reaction (PCR) leads to the conversion of uracil to thymine. Then, DNA material is sequenced. Since the reads’ strand is unknown in advance, mapping bisulfite-treated reads requires an approach that includes running four mapping processes simultaneously. Aim of this thesis was to develop a method for mapping bisulfite-treated reads to the reference genome. Since the problem of mapping bisulfite se- quences is essentially short read mapping problem, the developed tool in this paper relies on the newly developed mapper Accel-Align. Bisulfite mapper developed in this thesis is publicly available on Github and put under the MIT licence.
Keywords
Keywords (english)
Languageenglish
URN:NBNurn:nbn:hr:168:582319
Study programmeTitle: Computing
Study programme type: university
Study level: graduate
Academic / professional title: magistar/magistra inženjer/inženjerka računarstva (magistar/magistra inženjer/inženjerka računarstva)
Type of resourceText
File originBorn digital
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Created on2023-01-13 12:43:17