Primjena skrivenih Markovljevih modela za pretraživanje nukleotidnih sljedova

undergraduate thesis

• Title (english): Application of Hidden Markov Models for Searching Nucleotide Sequences
• Author: Krešimir Medvidović
• Mentor: Mirjana Domazet-Lošo (mentor)
• Committee member: Mirjana Domazet-Lošo (predsjednik povjerenstva)
• Committee member: Damir Kalpić (član povjerenstva)
• Committee member: Igor Mekterović (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

U ovom radu sam se pobliže upoznao s Markovljevim modelima i njihovom primjenom u bioinformatici. Nakon definiranja CpG otoka i skrivenih Markovljevih modela primjenio sam Viterbijev algoritam za pretragu CpG otoka u danom slijedu. Implementaciju sam napisao u programskom jeziku Java, te sam obavio testiranja ispravnosti programa, mjereći potrebno vrijeme i potrošnju radne memorije za izvođenje Viterbijevog algoritma. Dobiveni rezultati su u okvirima odstupanja od 10% u odnosu na promatrane programe CpG Islands (in VB6) i Sequence Manipulation Suite:CpG Islands.

Abstract (english)

In this thesis, I addressed the application of Markov’s Models in bioinformatics. I presented the problem of finding CpG Island using hidden Markov model (HMM). I applied the Viterbi’s algorithm for searching CpG Island in the following sequence. The program was implemented in the Java programming language. The program’s accuracy, speed and consumption of memory were tested. The results are within 10% deviation compared to the observed programs CpG Islands (in VB6) and Sequence Manipulation Suite: CpG Islands.

• Keywords: bioinformatika; Markovljevi modeli; skriveni Markovljevi modeli; CpG otoci; Viterbijev algoritam; nukleotidni sljedovi
• Keywords (english): bioinformatics; Markov process; Hiden Markov Models; CpG Island; Viterbi algorithm; nucleotide sequences
• Language: croatian
• URN:NBN: urn:nbn:hr:168:518474
• 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 22:56:30