Simulacija DNA sljedova korištenjem Gillespiejevog algoritma

undergraduate thesis

• Title (english): DNA sequence simulation based on Gillespie algorithm
• Author: Lucija Topolko
• Mentor: Mirjana Domazet-Lošo (mentor)
• Committee member: Mirjana Domazet-Lošo (predsjednik povjerenstva)
• Committee member: Mihael Kovač (član povjerenstva)
• Committee member: Andrej Slapničar (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2024-06-27, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Simulatori DNA sljedova ključni su alati u molekularnoj biologiji i bioinformatičkom istraživanju jer omogućuju simuliranje kompleksnih evolucijskih procesa kroz generacije. Ovi alati su od velikog značaja za istraživanje genetičke varijabilnosti, evolucijskih trendova i adaptivnih strategija organizama. U ovom radu razvijen je simulator temeljen na Gillespiejevom algoritmu. Gillespiejev algoritam predstavlja matematičku metodu za simulaciju stohastičkih procesa u biološkim sustavima. Ovaj simulator omogućava simulaciju DNA sljedova koristeći Jukes-Cantorov i Kimurin evolucijski model. Implementiran je u programskom jeziku C++, a testiran je na podacima virusa HIV-1. Rezultati su uspoređeni s rezultatima alata AliSim kako bi se provjerila njegova učinkovitost i pouzdanost.

Abstract (english)

DNA sequence simulators are key tools in molecular biology and bioinformatics research, as they enable the simulation of complex evolutionary processes across generations. These tools hold significant importance for studying genetic variability, evolutionary trends, and adaptive strategies of organisms. In this study, a simulator based on the Gillespie algorithm was developed. The Gillespie algorithm is a mathematical method for simulating stochastic processes in biological systems. This simulator allows for the simulation of DNA sequences using the Jukes-Cantor and Kimura evolutionary models. It was implemented in the programming language C++ and tested using HIV-1 virus data. The results were compared with those of the AliSim tool to verify its effectiveness and reliability.

• Keywords: bioinformatika; filogenetsko stablo; simulacija DNA sljedova; evolucijski modeli; Gillespiejev algoritam
• Keywords (english): bioinformatics; phylogenetic tree; DNA sequence simulation; models of evolution; Gillespie algorithm
• Language: croatian
• URN:NBN: urn:nbn:hr:168:136976
• 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: 2024-10-12 22:21:34