Thesis Details

Vyhledávání enzymů v metagenomických datech

Master's Thesis Student: Smatana Stanislav Academic Year: 2016/2017 Supervisor: Hon Jiří, Ing., Ph.D.
English title
Detection of Enzymes in Metagenomic Data
Language
Czech
Abstract

This thesis presents specification and implementation of a system for detection of enzymesin metagenomic data. The detection is based on a provided enzyme sequence and its goalis to search the metagenomic sample for its novel variants. In order to guarantee thatfound enzymes truly have the desired catalytic function, the system employs a number ofcatalytic function verification methods. Their specification, implementation and evaluationis one of the main contributions of this thesis. Experiments have shown, that proposedmethods reach sensitivity as high as 89%, specificity of 95%, values of AUC metric above0.9 and average throughput of 1,203 verifications per second on regular personal computer.Evaluation of the system also led to discovery of a partial sequence of novel haloalkanedehalogenase enzyme in a metagenomic sample from soil. The implementation is able towork on a personal computer as well as on a grid computing environment.

Keywords

metagenomics, enzymes, enzyme detection, catalytic function verification, catalytic site,novel enzymes, catalytic function, haloalkane dehalogenase, active site, catalytic residues

Department
Degree Programme
Information Technology, Field of Study Bioinformatics and Biocomputing
Files
Status
defended, grade A
Date
21 June 2017
Reviewer
Committee
Sekanina Lukáš, prof. Ing., Ph.D. (DCSY FIT BUT), předseda
Burgetová Ivana, Ing., Ph.D. (DIFS FIT BUT), člen
Horák Aleš, doc. RNDr., Ph.D. (FI MUNI), člen
Martínek Tomáš, doc. Ing., Ph.D. (DCSY FIT BUT), člen
Rogalewicz Adam, doc. Mgr., Ph.D. (DITS FIT BUT), člen
Zbořil František, doc. Ing., Ph.D. (DITS FIT BUT), člen
Citation
SMATANA, Stanislav. Vyhledávání enzymů v metagenomických datech. Brno, 2017. Master's Thesis. Brno University of Technology, Faculty of Information Technology. 2017-06-21. Supervised by Hon Jiří. Available from: https://www.fit.vut.cz/study/thesis/19850/
BibTeX
@mastersthesis{FITMT19850,
    author = "Stanislav Smatana",
    type = "Master's thesis",
    title = "Vyhled\'{a}v\'{a}n\'{i} enzym\r{u} v metagenomick\'{y}ch datech",
    school = "Brno University of Technology, Faculty of Information Technology",
    year = 2017,
    location = "Brno, CZ",
    language = "czech",
    url = "https://www.fit.vut.cz/study/thesis/19850/"
}
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