National Repository of Grey Literature 49 records found  1 - 10nextend  jump to record: Search took 0.00 seconds. 
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.
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.
Method for authentication Basmati type rice (Oryza sativa L.) using microsatellite length polymorphism: methodology for practice
Ovesná, Jaroslava ; Drábková, Lenka ; Kučera, Ladislav
The objective of the method is the proceudre how to identify traditional varieties of Basmati rice (TB) specified in the Implementing Regulation EU no. 706/2014 devoted to control laboratories in practice. This method enables to identify varieties exempt from duty in the EU. The test consists of microsatellite loci amplification by polymerase chain reaction (PCR) using specific primers, and subsequent analysis of the length of the products.
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Avian polyomaviruses
Škvára, Petr ; Fraiberk, Martin (advisor) ; Forman, Martin (referee)
Avian polyomaviruses are small, nonenveloped viruses from family Polyomaviridae, which can cause acute infection with high mortality of infected birds. In contrast with other polyomaviruses, avian polyomaviruses do not share similar pathogenesis, because most of them do not cause acute diseases. The main point of this work is to summarize available information about avian polyomaviruses and to compare them to each other. This work also compares avian polyomaviruses with mammalian polyomaviruses. The primary focus is made on genome organization, structure and function of viral proteins, but also on pathogenesis and epidemiology of avian polyomaviruses. In conclusion, even if avian polyomaviruses share common signs with other polyomaviruses, they have different conserved sequences, host specificity and pathogenicity. Summary of current knowledge about avian polyomaviruses could help to understand the importance of this newly established genus in the field of polyomavirus research. Key words: avian polyomaviruses, taxonomy, genome, viral proteins, pathogenesis
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.
Evoluce genomu bakteriálních symbiontů vši \kur{Polyplax serrata} (Phthiraptera, Anoplura)
ŘÍHOVÁ, Jana
Blood-sucking louse Polyplax serrata harbor two phylogenetically distinct symbiotic bacteria from the orders Legionellales (Gammaproteobacteria) and Neisseriales (Betaproteobacteria). Based on rigorous phylogenetic analyses, the first bacteria was confirmed as member of genus Legionella, and the name Candidatus Legionella polyplacis, sp. n. was proposed. Vertical transgeneration transmission was proved by visualisation of the symbiont in host tissues. Improved genome of latter symbiont is considerably larger and possesses more metabolic functions. In the genome, I found horizontally transferred operon, which encode synthesis of enzymes involved in urea cleavage.
Effective Search for Overlaps in NGS Data
Matocha, Petr ; Martínek, Tomáš (referee) ; Puterová, Janka (advisor)
The main theme of this work is the detection of overlaps in NGS data. The work contains an overview of NGS sequencing technologies that are the source of NGS data. In the thesis, the problem of overlapping detection is generally defined. Next, an overview of the available algorithms and approaches for detecting overlaps in NGS data is created. Principles of these algorithms are described herein. In the second part of this work a suitable tool for detecting approximate overlaps in NGS data is designed and its implementation is described herein. In conclusion, the experiments performed with this tool and the conclusions that follow are summarized and described.

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