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Management tool for sequence types database of pathogenic bacteria
Františová, Zuzana ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
The objective of this bachelor thesis is to design and create a management tool for sequence types database of pathogenic bacteria. The basis of this thesis is the designing a transfer key for the new molecular technique for typing of bacteria, which was created in cooperation with Centre of Molecular Biology and Gene Therapy, Department of Internal Medicine – Haematooncology, University Hospital Brno. The new method is based on translation sequence type to appropriate melt type. In the first two chapters, the advantages and disadvantages of the most used methods in molecular biology and the most favorite typing methods are discussed. Another three chapters introduce designing of the transfer key, its implementation in the MATLAB environment and the final management tool consisted of two programmes. The first program includes transfer key computation and the second program allows particular melt type and appropriate sequence types retrieval, which is an easy way to compare sequential and PCR data.
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Bacterial species delineation based on parameters derived from numerical representations of genome
Oweis, Kamil ; Jugas, Robin (referee) ; Maděránková, Denisa (advisor)
Modern methods of processing genomic data yield good results, however they are often redeemed by time consummation. This is mainly the reason why this thesis deals with numerical methods of bacterial genome processing which could be a suitable alternative for current methods, both in terms of quality and computational demands. This thesis presents the current methods used for processing of genomes in silico and proposes suitable numerical presentations for the whole genome analysis. Some of these methods are programmed and used for processing further in this diploma thesis. In it, various mathematical and statistical methods are being tested, ones that could lead to successful species delineation of bacteria by numerical presentations of their genomes.
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Detection of car accident and collapse by Android smartphone
Repčík, Tomáš ; Ronzhina, Marina (referee) ; Maděránková, Denisa (advisor)
Bachelor thesis “Detection of car accident and collapse by Android smartphone” describes theoretical basics of a collapse and a car accident. With help of 23 volunteers, data has been collected from daily tasks, simulating collapses and driving. Based on that a model with capability to classify a car accident was created. The detection of collapse uses neural network with accuracy of 86 %. The detection of car accident uses accelerometer and GPS. To indicate the car accident a high acceleration created by the accident and absence of moving car is required. Next, the application was tested by all available data and by the volunteers in daily life, who used the application for 520 h.
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Gene order conservation in bacterial genomes
Martinková, Tereza ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
Theoretical part of the thesis deals with basic concepts such as bacterial genome, comparative genomics and mainly synteny blocks. Here is explained what synteny is and what is its importance. In the theoretical part, the GenBank format is also mentioned, its content and usage. The practical part is focused on searching similarities in DNA sequences of reference bacteria with selected bacteria, their sorting by means of greedy algorithm and visualization of similarities using phylogenetic tree.
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Direct assembly of genome signals from nanopore sequencing
Karmazinová, Inna ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
The aim of this bachelor thesis is to search for overlaps between signals from nanopore sequencing using MinION device version R9. The theoretical part deals with methods used for genome assembly - greedy algorithm, overlap-layout-consensus (OLC) and de Bruijn graphs. Oxford Nanopore Technologies introduced the MinION device, which simplifies sequencing using the current change, which occurs while the DNA is passing through the nanopore. The error rate of the device is still high, the accuracy problem occurs during the base-calling. Using the difference signal, possibly also the dynamic time warping, it is possible to find overlaps between the individual signals. Signal analysis and genome assembly using the MinION signal could provide better accuracy.
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Synonymous codon usage bias in mitochondrial genomes
Urbanová, Hedvika ; Cicková, Pavlína (referee) ; Maděránková, Denisa (advisor)
This Bachelors thesis deals with synonymous codon usage bias in mitochondrial genomes. This thesis covers basic terms of bioinformatics and genetics. Codon usage bias is introduced together with parameters that characterize it. Practical part of the thesis is dealing with programs that are designed to calculate parameters of codon usage bias. Programs that are described in this thesis are relative synonymous codon usage, relative adaptation index, codon adaptation index, homozygosity of codons, and effective number of codons. Synonymous codon usage bias in mitochondrial genome of Homo sapiens is analysed.
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Pozitive and negative selection of mitochondrial genome
Svoboda, Matěj ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis deals with positive and negative selection detection in mitochondrial genome of invertebrates and vertebrates. The component of this paper is to interpret the theory of evolution and evolution models. The main objective of this bachelor thesis is to formulate the algorithm package for a positive and negative selection detection in a program environment, RStudio. Consequently, outcomes of algorithm are compared to values acquired by tool PAML.
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Evaluation of numerical representations suitability for overlap detection
Pleskačová, Barbora ; Maděránková, Denisa (referee) ; Jugas, Robin (advisor)
The bachelor´s thesis is focused on the evaluation of numerical representations suitability for overlap detection. Introductory part deals with description of deoxyribonucleic acid structure. The next part discribes sequencing methods and genome assembly techniques. Following part deals with numerical representations that convert DNA sequences into numerical form. Based on similarity metrics, the use of these representations is tested for the detection of overlaps between DNA reads. In the practical part of the thesis an algorithm for overlap detection is designed and implemented using numerical representations. The algorithm is then tested on data.
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Gene order conservation in bacterial genomes
Martinková, Tereza ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
Theoretical part of the thesis deals with basic concepts such as bacterial genome, comparative genomics and mainly synteny blocks. Here is explained what synteny is and what is its importance. In the theoretical part, the GenBank format is also mentioned, its content and usage. The practical part is focused on searching similarities in DNA sequences of reference bacteria with selected bacteria, their sorting by means of greedy algorithm and visualization of similarities using phylogenetic tree.
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