Memorijski učinkovita pohrana genoma iste vrste

undergraduate thesis

• Title (english): Memory-Efficient Storage of Multiple Genomes of the Same Species
• Author: Vinko Kodžoman
• Mentor: Mirjana Domazet-Lošo (mentor)
• Committee member: Mirjana Domazet-Lošo (predsjednik povjerenstva)
• Committee member: Boris Milašinović (član povjerenstva)
• Committee member: Petar Djerasimović (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2015-07-13, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

U ovom radu dajem svoje rješenje za memorijski i vremenski učinkovitu implementaciju prikaza kolekcije genoma kao i njihovog indeksiranja. Napravio sam indeks referentnog genoma baziran na BWBBLE, indeksu koji koristi Burrows-Whelerovou transformaciju. Kako bih povećao njegovu fleksibilnost, dodao sam promjenjive kodne tablice kao i ulazno/izlazni modul koji omogućuje stvaranje referentnog genoma iz populacije genoma. Indeks je napisan u programskom jeziku C++ i uspoređen sa BWA, programskim paketom za mapiranje sekvenci na referentne genome velike duljine. Indeks referentnog genoma nije konkurentan BWA-u u vremenu izvođenja, ali njegova veća fleksiblinost omogućuje korisniku stvaranje referentnog genoma i unos vlastitih kodnih tablica.

Abstract (english)

In this thesis I address the problem of memory-efficient representation of a collection of genomes and their indexing. I have developed a reference genome index based on a Burrows-Wheeler transform aligner called BWBBLE. To increase its flexibility, I have added custom code tables and created an input/output engine that enables creation of a reference genome from a genome population. The index is written in the C++ programming language and compared to BWA – a software package for mapping sequences against a large reference genome. The reference genome index is not competitive to the BWA performance-wise but it allows more flexibility, allowing the user to create a reference genome and input their own code tables.

• Keywords: Referentni genom; Indeks; Burrows-Wheelerova transformacija; Sufiksno polje; Pretraživanje uzoraka
• Keywords (english): Reference genome; Index; Burrows-Wheeler Transform; Suffix array; Pattern searching
• Language: english
• URN:NBN: urn:nbn:hr:168:739648
• 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: 2018-02-06 09:41:42