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undergraduate thesis
Poravnanje genoma korištenjem skrivenog Markovljevog modela
Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing, 2022. urn:nbn:hr:168:134344
Kuleš, Jurica
University of Zagreb
Faculty of Electrical Engineering and Computing

Institutional repository: FER Repository

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Kuleš, J. (2022). Poravnanje genoma korištenjem skrivenog Markovljevog modela (Undergraduate thesis). Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing. Retrieved from https://urn.nsk.hr/urn:nbn:hr:168:134344

Kuleš, Jurica. "Poravnanje genoma korištenjem skrivenog Markovljevog modela." Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2022. https://urn.nsk.hr/urn:nbn:hr:168:134344

Kuleš, Jurica. "Poravnanje genoma korištenjem skrivenog Markovljevog modela." Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2022. https://urn.nsk.hr/urn:nbn:hr:168:134344

Kuleš, J. (2022). 'Poravnanje genoma korištenjem skrivenog Markovljevog modela', Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, accessed 21 June 2024, https://urn.nsk.hr/urn:nbn:hr:168:134344

Kuleš J. Poravnanje genoma korištenjem skrivenog Markovljevog modela [Undergraduate thesis]. Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing; 2022 [cited 2024 June 21] Available at: https://urn.nsk.hr/urn:nbn:hr:168:134344

J. Kuleš, "Poravnanje genoma korištenjem skrivenog Markovljevog modela", Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb, 2022. Available at: https://urn.nsk.hr/urn:nbn:hr:168:134344

Metadata
TitlePoravnanje genoma korištenjem skrivenog Markovljevog modela
Title (english)Genome alignment based on hidden Markov model
AuthorJurica Kuleš
MentorMirjana Domazet-Lošo (mentor)
Committee memberMirjana Domazet-Lošo (predsjednik povjerenstva)
Committee memberIvica Botički (član povjerenstva)
Committee memberTomislav Jagušt (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Electrical Engineering and Computing
Zagreb
Defense date and country2022-09-06, Croatia
Scientific / art field,
discipline and subdiscipline		TECHNICAL SCIENCES
Computing
Abstract
U zadnjih nekoliko desetljeća, došlo je do značajnih pomaka u području genomike, ponajviše zahvaljujući bioinformatičkoj analizi, čiji je najčešći početni korak poravnanje genoma. U ovom radu naveo sam osnovne biološke pojmove iz područja genomike, predstavio osnovne mjere udaljenosti između bioloških sljedova te opisao Needleman-Wunschov algoritam za dobivanje optimalnog poravnanja dvaju sljedova. Najveći fokus bio je na matematičkom konceptu skrivenog Markovljevog modela i njegovoj primjeni na poravnanje dvaju genoma. Nadalje, predstavio sam tri glavna problema kod skrivenih Markovljevih modela i razradio njihova klasična rješenja. Opisao sam postupak procjene parametara modela, postupak izračuna optimalnog poravnanja korištenjem programskog jezika Python i biblioteke NumPy te proveo evaluaciju tako dobivenih rješenja. Također sam napravio analizu vremenske složenosti modela, ovisno o različitim veličinama ulaznog skupa podataka.
Abstract (english)
In the last few decades, there have been significant advances in the field of genomics, mostly thanks to bioinformatic analysis, whose most common initial step is genome alignment. In this paper I presented basic biological concepts in the field of genomics, basic measures of distance between biological sequences and described the Needleman-Wunsch algorithm for obtaining optimal alignment of two sequences. The main focus was on the mathematical concept of the hidden Markov model and its application to the alignment of two genomes. Furthermore, I laid down the three fundamental problems with hidden Markov models and elaborated their classical solutions. I described the procedure of estimating the model parameters and the procedure of calculating the optimal alignment using the Python programming language alongside the NumPy library and performed an evaluation of the solutions obtained in this way. I also made an analysis of the time complexity depending on the different sizes of the input data set of the model.
Keywords
Keywords (english)
Languagecroatian
URN:NBNurn:nbn:hr:168:134344
Study programmeTitle: 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)
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Created on2023-01-15 10:38:35