Analiza proteinskih motiva

master's thesis

• Title (english): Analysis of protein motifs
• Author: Igor Keserin
• Mentor: Pavle Goldstein (mentor)
• Committee member: Pavle Goldstein (predsjednik povjerenstva)
• Committee member: Bojan Basrak (član povjerenstva)
• Committee member: Goran Radunović (član povjerenstva)
• Committee member: Sonja Štimac (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Mathematics); Zagreb
• Defense date and country: 2023-11-30, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Mathematics

Abstract

U ovom diplomskom radu proučavamo problem klasifikacije proteina u proteinske familije. Motivi su kraći nizovi aminokiselina sa zajedničkim ulogom u organizmu. Često su evolucijski bolje očuvani dijelovi proteina te su time korisni za njihovu klasifikaciju. Testiramo i objašnjavamo metodu koja je razvijena za problem klasifikacije motiva. Metoda je implementirana kao nadogradnja standardnih tehnika pretraživanja motiva, gdje se, nakon ulaganja objekata u odgovarajući Euklidski prostor, koriste geometrijske metode optimizacije i strojnog učenja. Uspješnost postupka testiramo na 6 biljnih proteoma na kojima promatramo familiju WRKY transkripcijskih faktora. Metoda rezultira relativno uspješnom klasifikacijom, iako pretpostavka o međusobnoj bliskosti nije u potpunosti ispunjena.

Abstract (english)

In this thesis, we study the classification problem for protein families. Motifs are shorter sequences of amino acids with a common role in organisms. They are often better preserved parts of proteins and are useful for their classification. We test and explain a method that was developed for the motif classification problem. The method is implemented as an addition to standard motif searching techniques, where, after the transfer of objects to a corresponding Euclidean space, we use geometric optimization and machine learning methods. We test the success of the procedure on 6 plant proteomes in which we analyze the family of WRKY transcription factors. The method results in a relatively successful classification, although the assumption of mutual closeness is not fully fulfilled.

• Keywords: klasifikacija proteina; proteinske familije; Euklidski prostor; familijs WRKY
• Language: croatian
• URN:NBN: urn:nbn:hr:217:052504
• Study programme: Title: Mathematical Statistics; Study programme type: university; Study level: graduate; Academic / professional title: sveučilišni magistar matematike (sveučilišni magistar matematike)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2024-02-12 11:41:14