Određivanje modificiranih nukleotida koristeći sekvenciranje nanoporama i duboko učenje

master's thesis

• Title (english): Detection of Modified Nucleotides Using Nanopore Sequencing and Deep Learning Methods
• Author: Sanja Deur
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Tomislav Petković (član povjerenstva)
• Committee member: Krešimir Križanović (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2021-07-01, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

U ovome je radu razvijena metoda za detekciju modifikacija baza u DNA, koristeći sekvenciranje nanoporama i principe dubokog učenja. Sekvenciranje nanoporama detektira različite električne signale za različite nukleotide, za vrijeme prolaska DNA lanca kroz nanoporu. Zatim se provodi pretvorba detektiranih signala u DNA sekvencu. Nakon poravnanja očitanja na referencu, točke signala na mjestima insercija i delecija trebaju se remapirati, koristeći razvijenu metodu Remapper. Implementacija postiže značajne rezultate što se tiče vremena izvođenja, međutim s cijenom smanjenja točnosti. Izvorni kod dostupan je na https://github.com/sanjadeur/master-thesis/.

Abstract (english)

In this thesis, a method for DNA base modification detection is developed using Nanopore sequencing and deep learning principles. Nanopore sequencing detects different electrical current signals for different nucleotides, whilst a DNA strand passes through a nanopore. Then, basecalling is performed, translating the detected signals into a DNA sequence. After aligning basecalled reads to the reference, signal points at insertions and deletions should be remapped, using the developed Remapper method. The implementation achieves significant results regarding the runtime, though at the cost of reduced accuracy. Source code is available at https://github.com/sanjadeur/master-thesis/.

• Keywords: epigenetika; modifikacija DNA; 5mC metilacija; CpG kontekst; sekvenciranje nanoporama; duboko učenje
• Keywords (english): epigenetics; DNA modification; 5mC methylation; CpG context; Nanopore sequencing; deep learning
• Language: english
• URN:NBN: urn:nbn:hr:168:885246
• Study programme: Title: Computing; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka računarstva (magistar/magistra inženjer/inženjerka računarstva)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2023-01-13 12:06:16