Hibridna metoda sažimanja skupa genoma korištenjem referentnog genoma

undergraduate thesis

• Title (english): Hybrid referential genome compression
• Author: Jana Penić
• Mentor: Mirjana Domazet-Lošo (mentor)
• Committee member: Mirjana Domazet-Lošo (predsjednik povjerenstva)
• Committee member: Mario Brčić (član povjerenstva)
• Committee member: Mihael Kovač (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2023-06-30, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

S padanjem cijene sekvenciranja genoma, taj je postupak postao sve češći te zbog
toga količina genomskih podataka sve brže raste. To je dovelo do potrebe za učinkovitijim
načinima za pohranu i prijenos genomskih podataka te razvojem specijaliziranih
algoritama za sažimanje genomskih podataka. U ovom je završnom radu implementiran
algoritam za sažimanje Hybrid Referential Compression Method korištenjem programskog
jezika Python. HRCM koristi referentni genom za sažimanje drugih genoma
traženjem podudaranja sljedova nukleotida. U radu je objašnjen postupak sažimanja i
ekstrakcije podataka, korištene strukture podataka, utjecaj parametara na provođenje
sažimanja te su prikazani rezultati testiranja na različitim skupovima podataka.

Abstract (english)

As the cost of genome sequencing has fallen, this procedure has become more
common and, as a result, the amount of genomic data is rapidly growing. This has
led to the need for more efficient ways to store and transfer genomic data and for the
development of specialized algorithms for compressing genomic data. In this thesis,
the compression algorithm Hybrid Referential Compression Method is implemented
using the programming language Python. HRCM uses a reference genome to compress
other genomes by searching for matches in the nucleotide sequences. The thesis
explains the process of data compression and decompression, the used data structures,
the influence of parameters on the implementation of compression, and presents the
results of testing on different data sets.

• Keywords: algoritam; HRCM; sažimanje; kompresija; ekstrakcija; dekompresija; genom; Python
• Keywords (english): algorithm; HRCM; compression; decompression; genome; Python
• Language: croatian
• URN:NBN: urn:nbn:hr:168:262334
• 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: 2023-07-13 10:27:12