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National Repository of Grey Literature 12 records found  previous11 - 12  jump to record: Search took 0.01 seconds. 
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 Transposons
 Šurina, Oliver ; Martínek, Tomáš (referee) ; Puterová, Janka (advisor)
This thesis deals with the reconstruction of transposable elements based on an output of RepeaterExplorer. In the first section, this thesis introduces basics of molecular biology with focus on transposons and their structure. Then it describes design and implementation of application which reconstructs transposons based on an output of RepeatExplorer. Achieved results are presented by created interactive user interface. The application was then tesed in real enviroment. This thesis also delivers overview of existing tools for transposons identification.
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National Repository of Grey Literature : 12 records found   previous11 - 12  jump to record:
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2 Puterová, Jana
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