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Bioinformatics of human genome
Kupková, Karolína ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Bachelor thesis deals with DNA segments containing only adenine and guanine. The theoretical part describes the structure and composition of deoxyribonucleic acid, chromosomes and genes. There are basic informations about chimpanzees and the human genome and conformations of the chains containing adenine with guanine. The practical part consists of a program that searches for the required sections in sequence, it displays and saves it. The thesis includes analysis of genes which are common for humans and chimpanzees, which were analyzed to determine randomness, functionality a preserving of these sections.
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Similarity/dissimilarity analysis of genomic data on the basis of graphical representation
Těthal, Jiří ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
The work deals with the identification of species of animal through the density of nucleotids of mitochondrial gene CO1. In the first part the theory summarized information about DNA barcoding and the mitochondria, cellular organel that with this method is closely related. The second part deals with virtually comparing different sequences using the density of nucleotides. For this it was created program, which uses two functions, the first of the specified nucleotide sequence calculates the density and one can compare the density by distance methods.
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Detection of Genome Variations
Beluský, Tomáš ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
An influence of variations in human genome is perceptible at a first glance on human itself to see differences between the individuals and entire populations. Also, behavior or probability of certain diseases are influenced in large way by differences at genome's level. This work presents methods for detecting variations in the human genome that were developed after an arose of the second-generation sequencing technologies. A new tool that combines read pair and split read methods, with information about a depth of coverage was also designed and implemented. The tool was tested on simulated and real data and compared with a reference outputs.
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Comparison of mitochondrial DNA for species identification
Labounek, René ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
The work deals with the method of recognizing species on the analysis of mitochondrial DNA segment. This analysis and classification using segment gene called CO1 in literatures such as barcode of life. In the beginning of work is analyzed the mitochondrial theory of heredity and conditions of formation of barcode. Practical use is based on this theory in creating database of barcodes generated to different animal species. Data used for creating the library are drawn from public databases NCBI and BOLD Systems. The next part of this work concerns about methods of comparison of the individual barcodes to the others and especially to the barcode of human. Three main computing methods were used tore these analyses: Needleman-Wunsch algorithm, Smith- Waterman algorithm and comparison of similarities using distance matrix. This work also concerns about transformation of DNA molecule sequences from symbols to numeric formats, which is required for the distance matrix comparison method. Algorithms for searching for a barcode of a species and vice versa were created to ease the work with data.
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Fuzzy classification of DNA sequences
Těthal, Jiří ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The work deals with the fuzzy classification of DNA sequences. In the first part the theory summarized information about Fuzzy logic and methods of its use in the classification of biological sequence data. The second part is practically deal with the classification algorithm for assessing the similarity of sequences. Specifically, the dividing of coding and non-coding parts of the sequence and the use of fuzzy classification in DNA barcoding.
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Genetická a morfologická variabilita skupiny \kur{Melampyrum nemorosum}
DRAHNÍK, Petr
Melampyrum nemorosum agg. is very complicated group of hemiparasitic plants. According to the traditional concept, 15 species is distinguished. Recent molecular analyses show a need of critical taxonomic revision of group and a potential importance of ancient hybridization. Analysis of 3 regions of cpDNA (trnTUGU-trnLUAA, psbA-trnHGUG, rpl32-trnLUAG) and 2 regions of nuclear DNA (Agt1 and At103) reveals well supported lineage with limited geographical distribution. Morphology and genome size of genetically supported lineages were compared.
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Genetická a morfologická variabilita skupiny \kur{Melampyrum nemorosum}
DRAHNÍK, Petr
Melampyrum nemorosum agg. is very complicated group of hemiparasitic plants. According to the traditional concept, 15 species is distinguished. Recent molecular analyses show a need of critical taxonomic revision of group and a potential importance of ancient hybridization. Analysis of 3 regions of cpDNA (trnTUGU-trnLUAA, psbA-trnHGUG, rpl32-trnLUAG) and 2 regions of nuclear DNA (Agt1 and At103) reveals well supported lineage with limited geographical distribution. Morphology and genome size of genetically supported lineages were compared.
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The symbiotic bacteria of lice of genus \kur{Polyplax}: general phylogenetic and genomic characterisation
ŘÍHOVÁ, Jana
Blood-sucking lice of the genus Polyplax harbour two bacterial endosymbionts, one from family Legionellales and the other from family Neisseriales. Fylogenetic and genomic analyses reveal typical features of endosymbiotic bacteria and coevolution history with the host. In the genome of the endosymbiont from family Legionellales I found operon, which encodes biosynthesis of biotin, essential vitamin, especially for blood-sucking insects living on low-nutrient diet. This operon was probably horizontally transfer from Wolbachia, nutrient endosymbiont of bedbug Cimex lectularius.
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Geneticky podmíněné onemocnění degenerativní myelopatie psů
Křížová, Jana
Degenerative myelopathy i s an adult onset neurological disease mostly in dogs at old age. First signs are ataxia and weakness of hind legs due to demyelization and axon loss in the white metter of spinal cord. There is higher prevalence of the disease i some dog breeds such as German Shepherd Dog, Boxer and Pembroke Welsh Corgi. Studies have shown strong association between risk of developement of the disease and SOD1 gene mutations. SOD1:c.118G>A appears among wide range of breeds and SOD1:c.52A>T seems to be exclusive for Bernese Mountain Dog. SOD1 gene station causes similar neurological disease amongs humans called amyotrophic lateral sclerosis and degenerative myelopathy is the first spontanously onset model for amyotrophc lateral sclerosis.
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Dědičné onemocnění u koček
Kropáčková, Marcela
Bachelor work deals with Genetics with a view to hereditary disorder at domestic cats. There are described only some disorders that they have the most often occurrence, and are very important. The cats are divided according to age category, sex and genotype depending on occurrence these abnormalities. It is also referred about traits and next health disorders that are caused by mutation. There are briefly described the evolution and domestication of cats. It put bigger and emphatic attention on genome at these animals. Further, there are hold on genetics tests, by which we can determine, according to DNA variability, the predispositions for malfunctions and disorders in cats. The work starts from special articles and their results from study researches.
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