Izgradnja i vizualizacija filogenetskog stabla

undergraduate thesis

• Title (english): Phylogenetic tree construction and visualization
• Author: Lana Benčik
• 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

Podrijetlo i odnosi među vrstama proučavaju se stoljećima. Kako je vrijeme prolazilo, pojavile su se mnoge nove tehnologije koje su povukle nova područja studija. Jedno od tih područja je bioinformatika, disciplina koja se bavi prikupljanjem i analizom bioloških podataka. Potpodručje bioinformatike koje se naziva filogenija usredotočuje se na odnose među organizmima. Koristi različite metode za izračunavanje razlika u genetskom materijalu vrsta, a zatim ih vizualizira u obliku filogenetskih stabala. U ovom radu implementirala sam dvije metode koje koriste udaljenosti sekvenci aminokiselina različitih podtipova HIV virusa za konstruiranje filogenetskog stabla: UPGMA i Metodu povezivanja susjeda. Udaljenost dviju sekvenci izračunata je primjenom Jukes-Cantorovog korekcijskog modela na broj vidljivih razlika. Stabla se vizualiziraju jednostavnom manipulacijom i ispisom znakova koji predstavljaju čvorove i grane. Na kraju uspoređujem svoju vizualizaciju s onom iz Biopython modula.

Abstract (english)

The origin and relations between species have been studied for centuries. With the passage of time, many new technologies have emerged dragging along new fields of studies. One of those fields is bioinformatics, a discipline concerned with collecting and analyzing biological data. A subfield of bioinformatics called phylogeny focuses on relations between organisms. It uses different methods for calculating differences in the genetic material of species and then visualizes them in the form of phylogenetic trees. In this paper I have implemented two methods that use the distances of amino acid sequences of different HIV virus subtypes to construct a phylogenetic tree: UPGMA and Neighbor-Joining method. The distance of two sequences is calculated by applying Jukes-Cantor's correction model to the number of visible differences. Trees are visualized by simple manipulation and printing of characters that represent nodes and branches. In the end I compare my visualization to that of Biopython module.

• Keywords: bioinformatika; filogenija; filogenetsko stablo; geni; nukleotidi; proteini; aminokiseline; evolucijski modeli; Jukes-Cantorov model; Kimurin model; metode temeljene na udaljenosti; UPGMA; Metoda spajanja susjeda; sekvenciranje; poravnanje; Clustal Omega; čvorovi; korijen; roditelj; djeca; listovi; udaljenosti; grane; ukorjenjivanje srednje točke; Biopython; Newick
• Keywords (english): bioinformatics; phylogeny; phylogenetic tree; genes; nucleotides; proteins; amino acids; evolutionary models; Jukes-Cantor's model; Kimura's model; distance-based methods; UPGMA; Neighbor-Joining; sequencing; alignment; Clustal Omega; nodes; root; parent; children; leaves; distances; branches; mid-point rooting; Biopython; Newick
• Language: english
• URN:NBN: urn:nbn:hr:168:250491
• 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 09:56:03