Matrice udaljenosti, reducirani skriveni Markovljevi modeli i usporedba sekundarnih struktura proteina

master's thesis

• Title (english): Distance matrices, reduced Hidden Markov models and protein secondary structure comparison
• Author: Maja Zagorščak
• Mentor: Pavle Goldstein (mentor)
• Committee member: Damjan Franjević (predsjednik povjerenstva)
• Committee member: Pavle Goldstein (član povjerenstva)
• Committee member: Maja Matulić (član povjerenstva)
• Committee member: Mladen Kučinić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2012-12-20, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Tema rada je prepoznavanje supra-sekundarne strukture proteina kombinacijom metoda matrica udaljenosti i reduciranih skrivenih Markovljevih modela za profile. Na polipeptidnim lancima na kojima je prethodno anotirana supra-sekundarna struktura pomoću matrica udaljenosti, kombinacijom Position Specic Scoring Matrix (PSSM) tehnike i inverznog algoritma za računanje posteriornih vjerojatnosti, promatra se pridruzivanje između pozicija u modelu i pozicija u lancu. U rezultatima se vide jasne razlike u vrijednosti optimalnog pridruživanja za nizove koji sadrže supra-sekundarnu strukturu i nizove koji je ne sadrže. Na korištenim podacima, sličnost na razini tercijarne strukture uspješno je prepoznata kao udaljena homologija na primarnoj razini.

Abstract (english)

This work discusses recognition of protein supra-secondary structure by combining two methods: distance matrices (DM) and reduced profle Hidden Markov Models (rHMMp). Distance matrix method was frst used to detect supra-secondary structure elements in polypeptide chains. This was used to build a model (rHMMp), and an optimal model- sequence assignment was generated using Position Specifc Scoring Matrix (PSSM) and inverse posterior assignment (IPA) techniques. Results show a clear diference in optimal scores between sequences with supra-secondary structure elements and those without. It can be seen that, on data-sets used, structure similarity has been successfully recognized as distant homology at primary structure level.

• Keywords: primarna i supra-sekundarna struktura proteina; motivi; matrica udaljenosti proteina; matrica udaljenosti za parove sekundarnih struktura; inverzno
• Keywords (english): primary and supra-secondary protein structure; motifs; protein distance matrix; distance matrix for secondary structure pairs; inverse posterior assignment; PSSM
• Language: croatian
• URN:NBN: urn:nbn:hr:217:497937
• Study programme: Title: Molecular Biology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra molekularne biologije (magistar/magistra molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Access restricted to students and staff of home institution
• Created on: 2017-05-02 12:26:03