Sažimanje skupova genoma korištenjem referentnog genoma

undergraduate thesis

• Title (english): Referential compression of genomic data sets
• Author: Korina Šimičević
• Mentor: Mirjana Domazet-Lošo (mentor)
• Committee member: Mirjana Domazet-Lošo (član povjerenstva)
• Committee member: Nikica Hlupić (član povjerenstva)
• Committee member: Marina Bagić Babac (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

Sve bolje, preciznije i pristupačnije metode sekvenciranja uzrokovale su porast potražnje za sekvenciranjem, a time i generiranje sve većih skupova genomskih podataka. Javio se problem učinkovite pohrane podataka koji rješavaju razne metode kompresije. Općenitih metoda kompresije ima mnogo, međutim potrebne su specijalizirane metode koje uzimaju u obzir prirodu podataka koje sažimaju.
Hybrid Referential Compression Method (HRCM) je algoritam koji sažima genome zapisane u FASTA formatu te koristi sličnost genoma kako bi ih učinkovito pohranio koristeći referentni genom i tablicu raspršenog adresiranja.
U radu sam implementirala pojednostavljenu verziju HRCM algoritma te su napravila analize performansi algoritma u usporedbi s originalnom implementacijom. Također sam napravila dodatne analize performansi ovisno o različitim parametrima korištenim u algoritmu.

Abstract (english)

Increasingly better, more accurate and affordable sequencing methods have caused an increase in the demand for sequencing and thus the generation of ever-increasing sets of genomic data. There is a problem of efficient data storage that is solved by data compression. There are many general-purpose compression methods, but specialized methods are needed to take into account the nature of the data they are compressing.
The Hybrid Reference Compression Method (HRCM) is an algorithm that compresses genomes written in FASTA format and exploits genome similarity to efficiently store them using a reference genome and a hash table.
In this paper, I implemented a simplified version of the HRCM algorithm and compared its performance to original implementation. Additionally, I performed multiple analyses depending on the different parameters used in the algorithm.

• Keywords: kompresija genoma; referentni genom; Hybrid Referential Compression Method; tablica raspršenog adresiranja; k-meri
• Keywords (english): genome compression; reference genome; Hybrid Referential Compression Method; hash table; k-mer
• Language: croatian
• URN:NBN: urn:nbn:hr:168:280120
• 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: 2023-01-14 21:45:40