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Biological data averaging
Mlčoch, Marek ; Vítek, Martin (referee) ; Smital, Lukáš (advisor)
The thesis deals with the biological data averaging applied to a periodical and repetitive signal, specifically to an ECG signals. There were used signals from MIT-BIH Arrhythmia database and ÚBMI database. Averaging was realized with constant, floating and exponential Windows, where was used the method of addition of the filtered residue. This method is intended to capture the slow variations from the input to the output signal. The outcomes of these methods can be used as a basis for further work, or function as an example of principled methods. Methods and its outcomes were created in Matlab.
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Reconstruction of DNA Sequences Containing Repetitive Patterns
Dvořáček, Vojtěch ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
This bachelor thesis focuses on reconstruction of repetitive patterns in DNA sequences. Although it is motivated by need to create automated tool for telomere characterization in plant genomes, its goal is creating general solution of given problem. Suggested solution is based on k-mer analysis, which is alignment free method. Its greatest advantage lies in possibility to reconstruct repetitive patterns from NGS sequencing data. Within the scope of this work was designed and iplemented solution, which is able to automatically estiamte suitable parametres for k-mer analysis from input data and optimize them by local state space search method.
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Eucaryotic Genomes Comparison
Puterová, Janka ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
Main motive of this master thesis was the need of good bioinformatics tools for genome comparison and improvement of one of the existing tools - RepeatExplorer. This work offers an overview of transposable elements in DNA, existing tools for identification and analysis of repetitions in sequenced genomes, summary of currently used genome sequencing methods. This work describes shortcomings of RepeatExplorer tool with focus on comparative analysis of genomes. Two solutions to remove these problems were designed and implemented. The first solution is designed for comparing pairs of genomes. The principle of this solution is based on comparison of similarity of distribution of contigs coverages using Kolmogorov-Smirnov test, thanks to which we are able to determine different parts in the genomes.The second solution, which is used to compare multiple genomes, is based on the method of mapping reads from compared genomes to the reference genome contigs and provides contigs coverage graphs, by which we are able to determine the variability of the repeats.Their functionality was verified on real NGS data of organism Silene latifolia.
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J.K.Toole, Kurt Vonnegut, Jr. and Ken Kesey: Authority and Grotesque in the U.S. Literature of The 1960s.
Kocmichová, Linda ; Ulmanová, Hana (advisor) ; Sukdolová, Alice (referee) ; Olehla, Richard (referee)
The dissertation focuses on the impact of authority and grotesque in the U.S. literature of the 1960s. The key theoretical approaches used for the analysis were: Bakhtinian theory concerning popular carnival culture and Vizenor's theory concerning tricksters, Deleuzian notion of repetition and schizoanalysis and the theory of Foucault concerning power and anti- authority struggles. The main task of the analysis was to trace the common and differentiating features which were demonstrated in the novels in the form of anti-authority struggles and forms of madness, which is viewed as a deliberating force. The authors were chosen for their challenging attitudes toward the forms of power exercised over the American society and for the usage of the grotesque as a tool to convey a subversive message. The analysed authors were John Kennedy Toole and his A Confederacy of Dunces, Kurt Vonnegut Jr. and his Slaughterhouse 5 and Ken Kesey's One Flew Over the Cuckoo's Nest.
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Repetitive formations in Hindi
Diatka, Vojtěch ; Kostič, Svetislav (advisor) ; Hons, Pavel (referee)
The main goal of this bachelor thesis is systematization of classification of morphological operation known as repetition. Even elaborated studies on repetition either deal only with small part of this big topic or suffer from fragmentariness. After distinguishing repetition from reduplication we formulate definition for recognizing each case of examined phenomenon. Then we pursue the need to introduce theory of prototypes into thoughts about repetition that helps us to solve some problems concerning classification of this morphological operation. The greatest part of this thesis consists of classification of repetition itself. In introductory part of each chapter we briefly analyze the way in which other linguists treat the concrete type of repetition. Important two parts of each chapter are structural aspect and semantic aspect. By first we mean formal changes which word undergoes when reiterated. By the latter we mean semantic shifts. Both aspects are treated in detailed manner. Each type of repetition we exemplify by words taken from grammars and words taken from our corpus. Another important topic is onomatopoeic reduplication. We try to demonstrate why it is not type of reduplication and at the same time we propose how to account for this phenomenon. These words are best to describe when we...
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Eucaryotic Genomes Comparison
Puterová, Janka ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
Main motive of this master thesis was the need of good bioinformatics tools for genome comparison and improvement of one of the existing tools - RepeatExplorer. This work offers an overview of transposable elements in DNA, existing tools for identification and analysis of repetitions in sequenced genomes, summary of currently used genome sequencing methods. This work describes shortcomings of RepeatExplorer tool with focus on comparative analysis of genomes. Two solutions to remove these problems were designed and implemented. The first solution is designed for comparing pairs of genomes. The principle of this solution is based on comparison of similarity of distribution of contigs coverages using Kolmogorov-Smirnov test, thanks to which we are able to determine different parts in the genomes.The second solution, which is used to compare multiple genomes, is based on the method of mapping reads from compared genomes to the reference genome contigs and provides contigs coverage graphs, by which we are able to determine the variability of the repeats.Their functionality was verified on real NGS data of organism Silene latifolia.
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Reconstruction of DNA Sequences Containing Repetitive Patterns
Dvořáček, Vojtěch ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
This bachelor thesis focuses on reconstruction of repetitive patterns in DNA sequences. Although it is motivated by need to create automated tool for telomere characterization in plant genomes, its goal is creating general solution of given problem. Suggested solution is based on k-mer analysis, which is alignment free method. Its greatest advantage lies in possibility to reconstruct repetitive patterns from NGS sequencing data. Within the scope of this work was designed and iplemented solution, which is able to automatically estiamte suitable parametres for k-mer analysis from input data and optimize them by local state space search method.
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Biological data averaging
Mlčoch, Marek ; Vítek, Martin (referee) ; Smital, Lukáš (advisor)
The thesis deals with the biological data averaging applied to a periodical and repetitive signal, specifically to an ECG signals. There were used signals from MIT-BIH Arrhythmia database and ÚBMI database. Averaging was realized with constant, floating and exponential Windows, where was used the method of addition of the filtered residue. This method is intended to capture the slow variations from the input to the output signal. The outcomes of these methods can be used as a basis for further work, or function as an example of principled methods. Methods and its outcomes were created in Matlab.
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