Ručno određivanje lažnih preklapanja koja nastaju pri sastavljanju genoma

undergraduate thesis

• Title (english): Manual Detection of False Overlaps Occured During the Genome Assembly Process
• Author: Filip Floreani
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Krešimir Križanović (član povjerenstva)
• Committee member: Robert Vaser (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2017-07-10, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Proces sastavljanja genoma temeljen je na analizi preklapanja kratkih očitanja genetskog
materijala. Zbog očitanja loše kvalitete, kao i zbog prisutnosti kimernih i
ponavljajućih očitanja, osim ispravnih preklapanja pojavljuju se i lažna preklapanja.
Detekcija lažnih preklapanja ključna je u postizanju boljeg konačnog rezultata. Jedna
od metoda detekcije je generiranje 1D-signala temeljenog na izračunu broja preklapanja
svake nukleinske baze pojedinog očitanja, koji se potom prikazuje u obliku... More grafa.
Kroz ovaj rad predstavljeno je aplikacijsko rješenje za Android uređaje, kojim je moguće
označiti regije u kojima se pojavljuju lažna preklapanja, kao i sortirati grafove
po predefiniranim kategorijama. U radu je data teorijska osnova rješenja, kao i detalji
njegove implementacije i konačnog ispitivanja. Less

Abstract (english)

The genome assembly process is based on overlapping and analyzing short reads of
genetic information. False positive overlaps arise in addition to true positive overlaps,
as a result of low quality, chimeric and repetitive reads. Detection of these false positive
overlaps is key to constructing more accurate and complete genomes. One of the
methods for detecting such overlaps is by generating a 1D-signal based on the number
of overlaps of each nucleobase in a read, which can then be shown in... More the form of a chart.
This thesis presents an Android application for demarking areas of false overlaps on
the aforementioned charts, as well as sorting charts in predefined categories. Both the
theoretical and practical solution, as well as the testing process, have been documented
inside of this paper. Less

• Keywords: Lažna preklapanja; kimerna očitanja; ponavljajuća očitanja; sastavljanje genoma; Android; bioinformatika
• Keywords (english): False overlaps; chimeric reads; repetitive reads; genome assembly; Android; bioinformatics
• Language: croatian
• URN:NBN: urn:nbn:hr:168:489713
• Study programme: Title: 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 resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2019-03-13 20:15:15