Identifikacija periodičnosti višega reda u insektu Tribolium castaneum pomoću računalne grm metode

doctoral thesis

• Title (english): Identification of higher-order periodicity in insect Tribolium castaneum using computational grm method
• Author: Ines Vlahović
• Mentor: Vladimir Paar (mentor)
• Committee member: Matko Glunčić (predsjednik povjerenstva)
• Committee member: Vladimir Paar (član povjerenstva)
• Committee member: Đurđica Ugarković (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Physics); Zagreb
• Defense date and country: 2014-10-29, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Physics
• Universal decimal classification (UDC): 53 - Physics

Abstract

Koristeći računalnu metodu GRM, Global Repeat Map, u disertaciji sam analizirala genom insekta Tribolium castaneum, malog brašnara, kako bih identificirala periodičnosti višega reda (HOR-ove). Uz algoritme za detekciju tandemne DNK, koji rade na principu dinamičkih matrica poravnanja, kompresije podataka, mapiranja u numeričku sekvencu i FFT (Fast Fourier Transform), naša metoda čini učinkovit alat za analizu DNK sekvence. Prednost korištene metode, GRM, je u direktnom mapiranju DNK simboličke sekvence u frekventnu domenu stvarajući globalnu mapu te preko kompletnog ansambla „ključnih riječi“, s obzirom da nema ulaznih parametara, može identificirati repeticije svih duljina bez obzira da li postoje devijacije kopija od savršenog uzorka. Pomoću ove metode identificirala sam veliki broj periodičnosti višega reda u insektu T. castaneum koje su karakteristične za sisavce. Te periodičnosti višega reda zasnivaju se na monomerima duljina ~360 bp što su zapravo često istraživani sateliti insekta T.castaneum. Identifikacija HOR-ova je bitna za daljnja istraživanja regulatornih uloga tj. ekspresiji gena i u mehanizmima evolucijskog razvoja.

Abstract (english)

With GRM computational method, in thesis, I have analyzed insect Tribolium castaneum genome, in order to identify higher order repeats (HORs). Along the other algorithms for detection of tandem repeats, which works on principles of dynamical matrix alignments, data compression, mapping sequence in numerical one and Fast Fourier Transform, our method is effective tool for analysis a DNA sequence. Advantage of GRM method is in direct mapping of symbolic DNA sequence in frequency domain making global map and with the complete assemble of “key words”, with no input parameters, it can detect repeats of all lengths in spite of copy deviations of perfect sample. With this method I have identified a great number of higher order repeats in insect T.castaneum, which are characteristic for mammals. Those HORs are assembled from monomers of length ~360 bp, which are often investigated satellites of insect T.castaneum. Identification of HOR’s is relevant for further investigations of regulatory roles ie. gene expression and mechanisms of evolution development.

• Keywords: tandemne repeticije; periodičnosti višega reda – HOR; GRM – Global Repeat Map; Tribolium castaneum
• Keywords (english): tandem repeats; higher order repeats – HOR; GRM - Global Repeat Map; Tribolium castaneum
• Language: croatian
• URN:NBN: urn:nbn:hr:217:345197
• Study programme: Title: Physics; Study programme type: university; Study level: postgraduate; Academic / professional title: doktor/doktorica znanosti, područje prirodnih znanosti, polje fizika (doktor/doktorica znanosti, područje prirodnih znanosti, polje fizika)
• Type of resource: Text
• Extent: 119 str.
• File origin: Born digital
• Access conditions: Open access
• Created on: 2017-08-23 08:39:17