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Reconstruction of Repetitive DNA Segments
Bikár, Robert ; Lexa, Matej (referee) ; Martínek, Tomáš (advisor)
Hlavní motivací diplomové práce bylo najít vhodný algoritmus, který by vytvořil grafovou reprezentaci NGS sekvenačních dat v lineárním čase. Zvolenou metodou pro reprezentaci je de Bruijnův graf. V další části práce byl navrhnut nástroj, který je schopen transformovat graf do přijatelné podoby pro vykreslování, a dále je schopen odstraňovat chyby, které vznikají při konstrukci grafu. Cílem práce je vytvořit nástroj, který rekonstruuje repetitivní segmenty v DNA. Implementovaný nástroj byl otestován a je schopen identifikovat opakující se segmenty, určit jejich typy, vizualizovat je a sestavit jejich sekvenci na jednodušších genomech s velkou přesnotí. Při použití složitějších genomů, nástroj nalezne pouze fragmenty repetitivních segmentů.
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Binding of Cyanine Fluorescent Probes to DNA
ROMANCOVÁ, Ingrid
This master thesis is focused on theoretical study of the Cy3 and Cy5 dyes and their interactions with DNA. The main aim was to find the mot populated conformations of the Cy3-DNA and Cy5-DNA complexes. A comparison with the experimental structure was also done and the influence of the cyanine dyes on the conformational changes of the DNA chain was evaluated.
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Možnosti izolace nukleových kyselin v rostlinných a živočišných matricích
Truong, Thanh Huong
Isolation of nucleic acids is first step in most of molecule diagnosis. Literal abstract deals with various opportunities of nucleic acid isolation is the main part of this bachelor thesis. This work is about the most used methods from the oldest ones to the ones that are used nowadays. It covers methods such as salting in and salting out, chromatography, phenol -- chloroform extraction and isolation with magnetic particles. In the one of three chapters of literal abstract the basis of nucleic acids is described. Inhibitors for separation of nuclein acids are presented in another chapter of literal abstract. Minor part of the bachelor thesis deals with experimental process. The quality of the DNA acquired from various Cannabis sativa matrices are compared at two different weights of 20 mg and 100 mg. Evaluation of the results shows that use of 20mg oves us better quality.
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Metody izolace a archivace DNA z živočišných tkání
Dratvová, Lenka
n bachelor thesis methods of isolation and archiving of DNA from animal tissues I deal with different samples of animal tissues suitable for efficient isolation of DNA. It selected simple and modern methods of DNA isolation. The work also deals with the possibility of short-term and long-term storage of DNA with a description of the selected archival methods. The method of DNA compared in terms of quality, quantity, and labour, time and monetary perspectives. The individual methods of archiving are also evaluated at the end of the work. The work also includes a practical part, which deals with the isolation of DNA mainly from animal products (milk and milk products, blood, meat and meat products), but also other biological tissues. The procedure and results are presented in chapters "Material and Methods", and "Results and Discussion".
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Magnetic Nanoparticles for Targeted Delivery System of Plasmid into HEK293 cells
Bílek, Ondřej ; Svoboda, Ondřej (referee) ; Fohlerová, Zdenka (advisor)
This bachelor’s thesis deals with using of magnetic nanoparticles, SPIO nanoparticles and nanoparticles of commercial product MATra for transfection of ASAP plasmid into HEK293 cells and subsequent optimization of the process. The experimental part is enclosed with theorethical part that summarizes findings from the fields of synthesis of magnetic nanoparticles and their biomedical applications, theory dealing with possibilities of the insertion of foreign DNA or plasmids into the cell and of its efficiency evaluation.
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Transcription motif finding algorithms
Peřinová, Barbora ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis deals with finding transcription motifs in DNA sequences. The first part describes the DNA transcription process, the significance of transcription motifs and provides an overview of transcription motif databases. The second part contains the classification of transcription motif finding algorithms, and details seven existing algorithms. In the practical part, functions for the analysis according to the Oligo-Analysis algorithm were created. Created functions were validated on the artificially created sequences with introduced motifs. The analysis of two families of coregulated genes was realized and the results were compared with the values achieved by the authors of the Oligo-Analysis algorithm.
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Comparison of genomes by synteny block analysis
Pavel, Tomáš ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
The theoretical part of this bachelor thesis is aimed at basics of genetics. Term of gene and mutation are introduced in this section. There are gene and chromosome mutations mentioned and described. Following section is devoted to comparative genomics and especially to synteny. There is described what the synteny actually is and how the synteny arises. The end of the theoretical part of this thesis is about the evolution and there are described ways of sorting permutation vectors. The practical part of this bachelor thesis includes description of developed software. Output of this software is a dot-plot which shows detected synteny blocks. Indexes of these blocks are listed in GUI. The second important output is number of permutation steps. This number determines evolutionary distance between two analysed DNA sequences. The very last section is aimed at analyse of synthetic and real DNA sequences.
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Digital processing of plant genomes
Jugas, Robin ; Škutková, Helena (referee) ; Sedlář, Karel (advisor)
This work continues in development of DNA numerical representation’s field in the recent years. The aim of this bachelor thesis is to work out an overview of numerical representations of DNA sequences and to describe the differences and properties of nuclear and mitochondrial genetic code focused on plants. Final objective is analysis of usability these signal’s representations for classification of organisms. The theoretical part is focused on description of biological facts, overview of conversion methods of DNA sequences into signals, the methods of organisms classification and the DTW algorithm. The practical part contain the created GUI application for organism classification based on numerical sequences and the analysis of usability these numerical representations for classification. The outputs of cluster analysis of numerical sequences are compared with the phylogenetic tree.
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