Identification of higher-order periodicity in insect Tribolium castaneum using computational grm method

Vlahović, Ines (2014) Identification of higher-order periodicity in insect Tribolium castaneum using computational grm method. Doctoral thesis, Faculty of Science > Department of Physics.

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Abstract

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.

Item Type: Thesis (Doctoral thesis)
Keywords: tandem repeats, higher order repeats – HOR, GRM - Global Repeat Map, Tribolium castaneum
Supervisor: Paar, Vladimir
Date: 29 October 2014
Number of Pages: 119
Subjects: NATURAL SCIENCES > Physics
Divisions: Faculty of Science > Department of Physics
Depositing User: Gordana Stubičan Ladešić
Date Deposited: 28 Nov 2014 12:33
Last Modified: 28 Nov 2014 12:33
URI: http://digre.pmf.unizg.hr/id/eprint/3404

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