Thesis Details

Klasifikace bakterií do taxonomických kategorií na základě vlastností 16s rRNA

Master's Thesis Student: Grešová Katarína Academic Year: 2019/2020 Supervisor: Smatana Stanislav, Ing.
Language
Slovak
Abstract

The main goal of this thesis was to design and implement a tool that would be able to classify the sequences of the 16S rRNA gene into taxonomic categories using the properties of the 16S rRNA gene. The created tool analyzes all input sequences simultaneously, which differs from common classification approaches, which classify input sequences individually. This tool relies on the fact that bacteria contain several copies of the 16S rRNA gene, which may differ in sequence. The main contribution of this work is design, implementation and evaluation of the capabilities of this tool. Experiments have shown that the proposed tool is able to identify the corresponding bacteria for smaller datasets and determine the correct ratios of their abundances. However, with larger datasets, the state space becomes very large and fragmented, which requires further improvements in order for it to search the state space in an efficient way.

Keywords

metagenomics, 16S rRNA, copies of 16S rRNA gene, RNA secondary structure, taxonomic classification, Metropolis-Hastings

Department
Department of Computer Systems FIT BUT
Degree Programme
Information Technology, Field of Study Bioinformatics and Biocomputing
Files
Status
defended, grade A
Date
15 July 2020
Reviewer
Hon Jiří, Ing., Ph.D.
Committee
Sekanina Lukáš, prof. Ing., Ph.D. (DCSY FIT BUT), předseda
Bidlo Michal, doc. Ing., Ph.D. (DCSY FIT BUT), člen
Češka Milan, doc. RNDr., Ph.D. (DITS FIT BUT), člen
Jaroš Jiří, doc. Ing., Ph.D. (DCSY FIT BUT), člen
Kekely Lukáš, Ing., Ph.D. (DCSY FIT BUT), člen
Martínek Tomáš, doc. Ing., Ph.D. (DCSY FIT BUT), člen
Citation
GREŠOVÁ, Katarína. Klasifikace bakterií do taxonomických kategorií na základě vlastností 16s rRNA. Brno, 2020. Master's Thesis. Brno University of Technology, Faculty of Information Technology. 2020-07-15. Supervised by Smatana Stanislav. Available from: https://www.fit.vut.cz/study/thesis/22671/
BibTeX 
@mastersthesis{FITMT22671,
    author = "Katar\'{i}na Gre\v{s}ov\'{a}",
    type = "Master's thesis",
    title = "Klasifikace bakteri\'{i} do taxonomick\'{y}ch kategori\'{i} na z\'{a}klad\v{e} vlastnost\'{i} 16s rRNA",
    school = "Brno University of Technology, Faculty of Information Technology",
    year = 2020,
    location = "Brno, CZ",
    language = "slovak",
    url = "https://www.fit.vut.cz/study/thesis/22671/"
}

Theses

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