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Biological sequence classification utilizing lossless data compression algorithms
Kruml, Ondřej ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
Tato diplomová práce se zabývá možností využití bezeztrátových kompresních algoritmů ke klasifikaci biologických sekvencí. Nejdříve je představena literární rešerše o bezeztrátových kompresních algoritmech, která byla využita k výběru slovníkového algoritmu vytvořeného A. Lempelem a J. Zivem v roce 1976 (LZ77). Tento algoritmus je běžně používán k datové kompresi a v předkládané práci byl modifikován tak, aby umožnil klasifikaci biologických sekvencí. K algoritmu byly navrženy další modifikace, které rozvíjí jeho klasifikační možnosti. V průběhu práce byla sestavena sada datasetů biologických sekvencí, která umožnila podrobné testování algoritmu. Algoritmus byl porovnán s klasickými zarovnávacími metodami: Jukes-Cantor, Tamura a Kimura. Bylo ukázáno, že algoritmus dosahuje srovnatelných výsledků v oblasti klasifikace biologických sekvencí a dokonce je u 20% datasetů překonává. Lepší výsledky dosahuje zejména u sekvencí, jež jsou si vzájemně vzdálené.
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Evaluation of Organisms Relationship by Genomic Signal Processing
Škutková, Helena ; Tkacz, Ewaryst (referee) ; Schwarz,, Daniel (referee) ; Provazník, Ivo (advisor)
This dissertation deals with alternative techniques for analysis of genetic information of organisms. The theoretical part presents two different approaches for evaluation of relationship between organisms based on mutual similarity of genetic information contained in their DNA sequences. The first approach is currently standardized phylogenetics analysis of character based records of DNA sequences. Although this approach is computationally expensive due to the need of multiple sequence alignment, it allows evaluation of global and local similarity of DNA sequences. The second approach is represented by techniques for classification of DNA sequences in a form of numerical vectors representing characteristic features of their genetic information. These methods known as „alignment free“ allow fast evaluation of global similarity but cannot evaluate local changes. The new method presented in this dissertation combines the advantages of both approaches. It utilizes numerical representation similar to 1D digital signal, i.e. representation that contains specific trend along x-axis. The experimental part of dissertation deals with design of a set of appropriate tools for genomic signal processing to allow evaluation mutual similarity of taxonomically specific trends. On the basis of the mutual similarity of genomic signals, the classification in the form of dendrogram is applied. It corresponds to phylogenetic trees used in standard phylogenetics.
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Phylogeographic patterns and microevolutionary mechanisms in oceanic dolphins
Křišťanová, Žaneta ; Hulva, Pavel (advisor) ; Vokurková, Jana (referee)
This bachelor thesis discusses the current findings regarding the phylogeography of the Delphinidae family. It is mainly focused on phylogenetic structure and speciation of Delphinidae, as well as on the ways of differentiation of trophic niches and the evolution of ecotypes. In the past, the Pleistocene climate oscillation had a major influence on the development of individual species and populations. Currently, it is anthropogenic activities that cause fundamental changes in habitats and thereby change the living conditions for cetaceans. In several species of Delphinidae, the emergence of ecotypes has been recorded, where different populations of the same species use different ecological niches. This thesis is mainly dedicated to the ecotypes of the bottlenose dolphin (Tursiops truncatus). Variability in coloration, body length and spine morphology was noted for individual ecotypes. The spine is an important adaptation to the environment in Delphinidae. In this research, phylogenetic relationships between family of Delphinidae, life strategies and food niche of selected species of the genera Tursiops, Stenella and Delphinus are also described.
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Biological sequence classification utilizing lossless data compression algorithms
Kruml, Ondřej ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
Tato diplomová práce se zabývá možností využití bezeztrátových kompresních algoritmů ke klasifikaci biologických sekvencí. Nejdříve je představena literární rešerše o bezeztrátových kompresních algoritmech, která byla využita k výběru slovníkového algoritmu vytvořeného A. Lempelem a J. Zivem v roce 1976 (LZ77). Tento algoritmus je běžně používán k datové kompresi a v předkládané práci byl modifikován tak, aby umožnil klasifikaci biologických sekvencí. K algoritmu byly navrženy další modifikace, které rozvíjí jeho klasifikační možnosti. V průběhu práce byla sestavena sada datasetů biologických sekvencí, která umožnila podrobné testování algoritmu. Algoritmus byl porovnán s klasickými zarovnávacími metodami: Jukes-Cantor, Tamura a Kimura. Bylo ukázáno, že algoritmus dosahuje srovnatelných výsledků v oblasti klasifikace biologických sekvencí a dokonce je u 20% datasetů překonává. Lepší výsledky dosahuje zejména u sekvencí, jež jsou si vzájemně vzdálené.
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Evaluation of Organisms Relationship by Genomic Signal Processing
Škutková, Helena ; Tkacz, Ewaryst (referee) ; Schwarz,, Daniel (referee) ; Provazník, Ivo (advisor)
This dissertation deals with alternative techniques for analysis of genetic information of organisms. The theoretical part presents two different approaches for evaluation of relationship between organisms based on mutual similarity of genetic information contained in their DNA sequences. The first approach is currently standardized phylogenetics analysis of character based records of DNA sequences. Although this approach is computationally expensive due to the need of multiple sequence alignment, it allows evaluation of global and local similarity of DNA sequences. The second approach is represented by techniques for classification of DNA sequences in a form of numerical vectors representing characteristic features of their genetic information. These methods known as „alignment free“ allow fast evaluation of global similarity but cannot evaluate local changes. The new method presented in this dissertation combines the advantages of both approaches. It utilizes numerical representation similar to 1D digital signal, i.e. representation that contains specific trend along x-axis. The experimental part of dissertation deals with design of a set of appropriate tools for genomic signal processing to allow evaluation mutual similarity of taxonomically specific trends. On the basis of the mutual similarity of genomic signals, the classification in the form of dendrogram is applied. It corresponds to phylogenetic trees used in standard phylogenetics.
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Biology and diversity of Cryptosporidium infecting squirrels (Sciuridae)
BARVÍŘ, Pavel
In total 399 samples from three species of squirrels (Sciurus vulgaris, Sciurus carolinensis and Callosciurus finlaysonii) were collected from 2010 to 2013. All samples were examined for the presence of Cryptosporidium using by molecular methods, which demonstrated by presence of Cryptosporidium specific DNA in 18 samples (4.5%). Out of them 12 samples were positive onCryptosporidium ferret genotype, 3 on Cryptosporidium skunk genotype, 1 on Cryptosporidium chipmunk genotype I and 2 samples onCryptosporidium ubiquitum. Statistical analyses did not reveal any influence of gender on the occurrence of Cryptosporidium. Juvenile individuals of squirrels from the family Sciuridae are more often infected by Cryptosporidium than the adult animals.
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