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Methods of processing Oxford Nanopore sequencing data for metagenomics
Barilíková, Lujza ; Provazník, Ivo (referee) ; Kupková, Kristýna (advisor)
The revolutionary sequencing technology introduced by Oxford Nanopore Technologies – MinION holds a great promise in the field of metagenomics. Low cost, produced long reads and portability, due to its small dimensions, represents only one of the many advantages of this technology. Despite the benefits, there is a lack of available computational tools for handling the produced data. The theoretical part of the thesis first introduces current sequencing technologies with main focus on the third-generation sequencing and especially on nanopore sequencing. The recent possibilities of metagenomic data visualization are introduced. The main purpose of the bachelor thesis is to make an algorithm for binning of metagenomic samples based on use of dimensionality reduction techniques straight on raw data produced by nanopore sequencing.
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Pozitive and negative selection of mitochondrial genome
Svoboda, Matěj ; Kupková, Kristýna (referee) ; Maděránková, Denisa (advisor)
The bachelor thesis engages with problematics of positive and negative selection of mitochondrial genome. Thesis is divided into two parts. First part grapples with theory and explanation of fundamental definitions, in particular understates mitochondrial genome, nucleotide mutation, positive and negative selection and furthermore evolution models. Second part focuses on processing mitochondrial DNA practically and on establishing functions in programming environment R. The emphasis is foremost on gene sequencing alignment and exploring substitutions. Consequently, obtained outcomes are contrasted with PAML and KaKs Calculator programme outcomes.
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Sleep stage classification based on Hjorth descriptors of EEG signals
Kupková, Kristýna ; Ronzhina, Marina (referee) ; Kozumplík, Jiří (advisor)
This bachelor thesis is focused on the distinction between sleep stages from EEG signals. In its first part the classical method of visual classification of sleep stages is introduced, the second part introduces an automated method for sleep stage scoring. It is a method that uses the three parameters of Hjorth to create a vector space, in which, on the basis of similarity of formed shapes, different stages of sleep could be distinguished. Parameters of Hjorth are calculated from the whole EEG signal, and also from its bands. In the next section of this thesis a principle component analysis is performed. The principle components are placed into a vector space analogously with parameters of Hjorth and the character of formed objects is observed.
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Methods for fast sequence comparison and identification in metagenomic data
Kupková, Kristýna ; Škutková, Helena (referee) ; Sedlář, Karel (advisor)
Předmětem této práce je vytvoření metody sloužící k identifikaci organismů z metagenomických dat. Doposud k tomuto účelu spolehlivě dostačovaly metody založené na zarovnání sekvencí s referenční databází. Množství dat ovšem s rozvojem sekvenačních technik rapidně roste a tyto metody se tak stávají díky své výpočetní náročnosti nevhodnými. V této diplomové práci je popsán postup nové techniky, která umožňuje klasifikaci metagenomických dat bez nutnosti zarovnání. Metoda spočívá v převedení sekvenovaných úseků na genomické signály ve formě fázových reprezentací, ze kterých jsou následně extrahovány vektory příznaků. Těmito příznaky jsou tři Hjorthovy deskriptory. Ty jsou dále vystaveny metodě maximalizace věrohodnosti směsi Gaussovských rozložení, která umožňuje spolehlivé roztřídění fragmentů podle jejich příslušnosti k organismu.
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The Transfer Pricing in Selected Business Enterprise
KUPKOVÁ, Kristýna
This diploma thesis deals with the issue of transfer pricing. Based on the performed functional, risk and comparative analysis, it proposes recommendations to the company leading to the elimination or mitigation of identified risks. The selected enterprise and its group are characterized by performing a functional and risk analysis, it is characterized and on this basis the transactions taking place within the group are analyzed. These transactions are compared with the market environment of comparable companies. On the basis of the calculated market profit range, conclusions are made about compliance with the market distance principle. Part of the overall analysis is also an analysis of the comparison of margins for products sold within the group, which is also compared with the margins charged to unrelated parties to explain the sales strategy of the selected company. According to the information obtained from the analysis of the company's financial environment, the main risks to the company resulting from the market environment and poorly set transfer pricing policy are outlined. After carrying out the given procedure, it was found that the company complies with the principle of market distance in the examined years, however, the business policy setting requires the introduction of strict control over the future development of the transfer price.
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Czech(oslovak)-Israeli Relations from 1945 till today
Kupková, Kristýna ; Kalhousová, Irena (advisor) ; Konrád, Ota (referee)
The presented bachelor thesis deals with the changes in diplomatic approaches between the Czechoslovak or Czech Republic and the State of Israel. The thesis examines the period since the end of World War II in 1945 up to the present i.e., the first twenty years of the 21st century. The work is divided into five chapters, which correspond to the various time periods of mutual relations. The aim of this work is to examine five different time periods and capture their characteristic phenomena and influences in order to determine which factors were or are most active in the Czecho(slovak)-Israeli relationship, and whether they had changed throughout history or even are still altering. The thesis presents both international and national influences and therefore focuses on the international political position of Czechoslovakia or the Czech Republic in the global order, as well as on the formation of internal politics and the position of the social organization. The thesis uses the methods of case studies, analysis of secondary sources and comparisons, through which in the summary of the thesis it detects changes in the given five periods.
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Signal Based Processing Of Metagenomic Data From Nanopore Sequencing
Kupková, Kristýna
The revolutionary sequencing technology introduced by Oxford Nanopore Technologies – MinION holds a great promise in the field of metagenomics due to its low cost, produced long reads and small size, which makes it available also for field work. The only problem preventing this technology from reaching its full potential is the lack of available computational tools for handling the produced data. Here we present an algorithm for processing of the raw signal sequences generated by nanopore sequencing for metagenomic purposes allowing to remove viral sequences from a contaminated metagenomic sample.
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Alignment-free Visualization of Metagenomic Data by Genomic Signal Processing
Kupková, Kristýna
Alignment-free visualization of metagenomic data without prior knowledge about organism composition is one of the major issues in metagenomic bioinformatics. Such a visualization method must place fragments from one organism in close proximity to each other, be reproducible and with rapidly increasing amount of data also work ideally in linear time. A novel technique fulfilling all of these requirements is introduced in this paper. The method is based on transformation of genomic sequence into phase signal representation with extraction of three Hjorth’s descriptors forming three dimensional space for visualization.
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Methods of processing Oxford Nanopore sequencing data for metagenomics
Barilíková, Lujza ; Provazník, Ivo (referee) ; Kupková, Kristýna (advisor)
The revolutionary sequencing technology introduced by Oxford Nanopore Technologies – MinION holds a great promise in the field of metagenomics. Low cost, produced long reads and portability, due to its small dimensions, represents only one of the many advantages of this technology. Despite the benefits, there is a lack of available computational tools for handling the produced data. The theoretical part of the thesis first introduces current sequencing technologies with main focus on the third-generation sequencing and especially on nanopore sequencing. The recent possibilities of metagenomic data visualization are introduced. The main purpose of the bachelor thesis is to make an algorithm for binning of metagenomic samples based on use of dimensionality reduction techniques straight on raw data produced by nanopore sequencing.
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