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Effective Dynamic Programming in Bioinformatics
Franěk, Jaromír ; Hynek, Jiří (referee) ; Burgetová, Ivana (advisor)
Purpose of this thesis is to study principle of effective algorithms, that are using dynamic programming. Using this knowledge to create application demonstrating principle of effective algorithm of dynamic programming in bioinformatics and write a report summarizing results. Algorithms used in this thesis are solving DNA sequence alignment or RNA secondary structure prediction. These algorithms are compared between themselves based on different input values. For DNA sequence alignment are used algorithms such as Needleman-Wunch and X-drop. For prediction of secondary RNA structure is used Zuker algorithm, that should remove some of Nussin algorithm weaknesses and Nussin algorithm itself. Recursion is showed by recursion trees. Dynamic programming is showed by score matrix. User also have ability to compare speed of both approaches for given sequences. It is programmed as web application, that run on client's side. This ensure easy availability.
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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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Bioinformatic Tool for Classification of Bacteria into Taxonomic Categories Based on the Sequence of 16S rRNA Gene
Valešová, Nikola ; Hon, Jiří (referee) ; Smatana, Stanislav (advisor)
Tato práce se zabývá problematikou automatizované klasifikace a rozpoznávání bakterií po získání jejich DNA procesem sekvenování. V rámci této práce je navržena a popsána nová metoda klasifikace založená na základě segmentu 16S rRNA. Představený princip je vytvořen podle stromové struktury taxonomických kategorií a používá známé algoritmy strojového učení pro klasifikaci bakterií do jedné ze tříd na nižší taxonomické úrovni. Součástí práce je dále implementace popsaného algoritmu a vyhodnocení jeho přesnosti predikce. Přesnost klasifikace různých typů klasifikátorů a jejich nastavení je prozkoumána a je určeno nastavení, které dosahuje nejlepších výsledků. Přesnost implementovaného algoritmu je také porovnána s několika existujícími metodami. Během validace dosáhla implementovaná aplikace KTC více než 45% přesnosti při predikci rodu na datových sadách BLAST 16S i BLAST V4. Na závěr je zmíněno i několik možností vylepšení a rozšíření stávající implementace algoritmu.
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Evaluation of numerical representations suitability for overlap detection
Pleskačová, Barbora ; Maděránková, Denisa (referee) ; Jugas, Robin (advisor)
The bachelor´s thesis is focused on the evaluation of numerical representations suitability for overlap detection. Introductory part deals with description of deoxyribonucleic acid structure. The next part discribes sequencing methods and genome assembly techniques. Following part deals with numerical representations that convert DNA sequences into numerical form. Based on similarity metrics, the use of these representations is tested for the detection of overlaps between DNA reads. In the practical part of the thesis an algorithm for overlap detection is designed and implemented using numerical representations. The algorithm is then tested on data.
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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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Genetická diverzita zástupců čeledi sezamovitých Pedaliaceae R.Br.
Šlampa, Vojtěch
The family Pedaliaceae belonging to the order Lamiales, described in 1810 by Robert Brown, is an important part of the tropical flora, which can be found mainly in Africa, Sou-theast Asia, and Australia. The family itself has 50 species and has not yet been studied very closely, except for the genus Sesamum and its representative Sesamum Indicum L., which is among the most important crops for food purposes. In this work, five representatives of the Pedaliaceae family were analyzed using the DNA barcoding method, using nuclear and chlo-roplast DNA regions, which served as a marker for their subsequent phylogenetic analysis and taxonomic classification. DNA isolation from plant samples, PCR, and DNA sequencing was performed to obtain plant DNA and the necessary results.
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Diversity of European freshwater cyclopoid species: phylogeny, morphology and ecology
Krajíček, Martin ; Černý, Martin (advisor) ; Brancelj, Anton (referee) ; Wyngaard, Grace (referee)
Cyclopoids are together with Calanoids and Harpacticoids a part of the largest, very diverse group of crustaceans and the most numerous aquatic metazoans of the world. The history of their research goes as far back as to the beginning of 19th century when the first cyclopoid copepods were described. The taxonomy of cyclopoids started to develop gradually since that time, adding new and more detailed methods and morphological characters, as well as a certain degree of taxonomical confusion. In last decades, the molecular-genetic techniques of DNA sequencing have become available offering a new independent tool for taxonomists. This work contains different studies concerning the morphology, taxonomy, ecology, distribution and colonisation of cyclopoid copepods, with the use of molecular tools as a uniting element. Chapter 1 of this thesis summarizes basic knowledge about the taxonomy, morphology and biology of cyclopoid copepods and introduces the following chapters containing four studies presented as single publications. The taxonomy of copepods of the genus Cyclops is based mainly on the morphology which is sometimes ambivalent and some of the most problematic species groups are presented here. Chapter 2 presents our unique results, the first reconstruction of phylogenetic relationships among 15...
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Preparation of a library of methionine sulfoxide reductase for applications in synthesis of chiral sulfoxides
Havelka, Václav ; Míšek, Jiří (advisor) ; Hlouchová, Klára (referee)
Chiral sulfoxides are important compounds in the pharmaceutical and chemical industries, however, their enantioselective synthesis providing only one desired enantiomer is not fully mastered. Some natural enzymes can be used for the biocatalytic preparation of chiral sulfoxides. One of such enzymes is methionine sulphoxide reductase. Methionine sulphoxide reductase is an enzyme limiting the effects of reactive oxygen radicals in the organism resulting from oxygen metabolism. Its function is the reduction of methionine sulfoxide in proteins to methionine. There are two types of methionine sulphoxide reductase, methionine sulphoxide reductase A reducing only (S)-methionine sulphoxide and methionine sulphoxide reductase B reducing (R)-methionine sulphoxide. Methionesulfoxide reductase B is suitable for the preparation of (S)-sulfoxides, however its catalytic activity is not sufficient for practical use. Using the recombinant DNA and mutagenic PCR techniques, a methionine sulphoxide reductase B mutant library was prepared, and the extent and nature of mutation introduced was determined. This library will serve as a starting point for the controlled evolution of the enzyme to obtain clones with increased activity and reduced substrate specificity.
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Targeted next generation sequencing of candidate genes responsible for impaired spermatogenesis and male infertility
Daňková, Michaela ; Liška, František (advisor) ; Holá, Dana (referee)
Infertility is a widespread health problem, caused by the male factor in about half of all cases, and in about a half of the infertile men the cause is unknown. In a significant number of these men, genetic etiology is assumed. Current routine methods of laboratory diagnostics, which include karyotype examination, exclusion of mutations in the CFTR gene, and Y chromosome microdeletions, do not usually reveal the cause of infertility. That is why researchers' efforts aim at detecting mutations in other genes that are causing male infertility. In recent years, animal models have been used to identify many genes necessary for fertility. Based on these findings, 12 candidate genes have been selected (CAPZA3, CDC14B, CDC42, CNTROB, CSNK2A2, GOPC, HOOK1, HRB, OAZ3, ODF1, RIMBP3, SPATA16) that are essential for spermatogenesis. Mouse or rat mutants in these genes are primarily associated with oligoasthenoteratozoospermia, since they are involved in sperm morphogenesis. However, the phenotype spectrum may comprise also azoospermia. The purpose of the thesis was to determine the sequence of the afore mentioned genes in infertile men with impaired spermatogenesis and to reveal presence or absence of pathogenic mutations in these genes, using cDNA and genomic DNA from peripheral blood. The candidate genes were...
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The analysis of immunoglobulin and T-cell receptor gene rearrangements using next generation sequencing
Hašek, Daniel ; Froňková, Eva (advisor) ; Javorková, Eliška (referee)
DNA sequencing is a molecular genetic method that results in data about sequence and type of nucleotides present in a given sample of deoxyribonucleic acid (DNA), a molecular carrier of genetic information. These data are frequently of a crucial value for many fields; research, medicine, industry, criminalistics or others. During a long period of time almost all the sequencing was performed using a method invented by Frederick Sanger in the 70's, a technique that uses modified nucleotides that once incorporated into a DNA strand prevent this from further elongation. DNA synthesis in presence of such nucleotides leads to a formation of a mixture of fragments of different lenght that are electrophoretically separated by lenght and the sequence is read from the resulting gel. Since the principle of this method entails some inherent drawbacks (e.g. low throughput and coverage) a significant effort is made lately to develop alternative sequencing approaches. These methods colectively refered to as next-generation sequencing (NGS) use several technologies in order to overcome the limitations of the Sanger sequencing. This thesis discusses the most important NGS methods and focuses on their possible application for sequencing of immunoglobulin and T-cell receptor gene rearrangements, an area of undisputable...
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