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Comparison of genomes by synteny block analysis
Pavel, Tomáš ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
The theoretical part of this bachelor thesis is aimed at basics of genetics. Term of gene and mutation are introduced in this section. There are gene and chromosome mutations mentioned and described. Following section is devoted to comparative genomics and especially to synteny. There is described what the synteny actually is and how the synteny arises. The end of the theoretical part of this thesis is about the evolution and there are described ways of sorting permutation vectors. The practical part of this bachelor thesis includes description of developed software. Output of this software is a dot-plot which shows detected synteny blocks. Indexes of these blocks are listed in GUI. The second important output is number of permutation steps. This number determines evolutionary distance between two analysed DNA sequences. The very last section is aimed at analyse of synthetic and real DNA sequences.
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Pozitive and negative selection of mitochondrial genome
Svoboda, Matěj ; Kupková, Kristýna (referee) ; Maděránková, Denisa (advisor)
The bachelor thesis engages with problematics of positive and negative selection of mitochondrial genome. Thesis is divided into two parts. First part grapples with theory and explanation of fundamental definitions, in particular understates mitochondrial genome, nucleotide mutation, positive and negative selection and furthermore evolution models. Second part focuses on processing mitochondrial DNA practically and on establishing functions in programming environment R. The emphasis is foremost on gene sequencing alignment and exploring substitutions. Consequently, obtained outcomes are contrasted with PAML and KaKs Calculator programme outcomes.
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Digital signal processing of mitochondrial genomes
Sonnenschein, Jiří ; Vítek, Martin (referee) ; Škutková, Helena (advisor)
The aim of this thesis is to test new less hardware demanding method of mitochondrial genom classification, for which numerical representation of biological sequences is used. Introductory part is focused on description of nucleic acids and mitochondrion. In following part of thesis, types of numerical representation of biological sequences without losing the original biological information are described. There are introduced possibilities of phase and frequency-domain analysis and principles of cluster analysis and dendrogram construction methods. Practical part of this work deals with analysis of mitochondrial genome for which cumulated and unwrapped phases are calculated. Mitochondrial sequences are compared by cluster analysis and dendrogram is constructed.
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Operon structures inference in genome-wide analysis
Nejezchlebová, Julie ; Jurečková, Kateřina (referee) ; Schwarzerová, Jana (advisor)
The bachelor thesis is devoted to the problem of derivation of operon structures and creation of a software tool that allows prediction of operon structures. The tool both predicts operons based on gene expression information, but also refines already predicted operons with gene expression information. The tool is tested on the bacteria Escherichia coli BW25113 and Clostridium beijerinckii NRRL B-598. The theoretical part is devoted to description of operon structure and function, genome sequencing, transcriptome analysis, Clostridium beijerinckii NRRL B-598, Escherichia coli BW25113 and already available online tools for inferring operon structures. In the practical part of the thesis, the pre-processing of raw transcriptomic data to obtain a suitable format for the prediction of operon structures, testing of online tools and the actual implementation of the tool itself are discussed.
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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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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.
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Identifying CpG islands in genomes of eukaryotes
Urbánková, Kateřina ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Bachelor thesis deals with searching CpG islands in DNA. The theoretical part describes the structure and composition of deoxyribonucleic acid, chromosomes and genes. There is basic information about human and chimpanzees genome and specification of CpG islands. Practical part consists of a program that searches for CpG islands in sequences, it displayes and saves it. This work includes analysis of genes which are common for Homo sapiens, Pan troglodytes, Mus musculus and Bos taurus.
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Karyotype evolution of cobweb spiders (Araneae: Theridiidae)
Večeřová, Hana ; Forman, Martin (advisor) ; Dolejš, Petr (referee)
Spiders (Araneae) are diversified order of the subphylum Chelicerata. Majority of the order belongs to group Entelegynae, as well as representatives of cobweb spider family (Theridiidae). Their noteworthy genus is Latrodectus, also known as "black widows". This thesis summarizes basic information about the genus, it's biology, phylogenetics and cytogenetics, with an overlap to genomics of cobweb spiders and their related species. Even though spiders' cytogenetics is an interesting field, particularly due to the occurance of unusual systems of sex chromosomes, some of the questions remain unanswered. A leading trend in entelegyne spiders is the reduction of diploid counts, where most mechanisms of the process remains unclear. Main aim of the thesis was to verify a potential of cobweb spiders as a model system for future studies of these changes. The genus Latrodectus may have potential because of showing suprisingly diverse karyotypes, which is unusual in Entelegynae. Despite their popularity, quality of karyotype data is poor and deserves to be revised. Nevertheless, the cosmopolitan L. geometricus is purposed as a keypart of promising model system for comparison of genome with modern cytogenomic approaches. Establishment of such model system could adress the questions about mechanism of karyotype...
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Hybridisation of cyprinid fishes in the Czech Republic: genetic and morphometric analysis of the subfamily Leuciscinae
Kaufman, Vít ; Musilová, Zuzana (advisor) ; Choleva, Lukáš (referee)
Hybridization is a process when two interspecific individuals mate and spawn. When backcrossing it often goes hand in hand with admixing unrelated genome into the genome of a species. Nowadays it is well established that hybridization is not as uncommon as it was believed. Especially in vertebrates fish are quite common in such phenomena. In Leuciscids, the family of order Cypriniformes is relatively frequent. It is a rife family in the European freshwater systems. Factors that contribute to such frequent hybridization are extraneous fertilization, sympatric occurrence, competition for spawning grounds, and other ecophysiological traits. It was known since the second half of 20th century that this is an ongoing phenomenon in many species of this family. Previous research was focused mainly on morphological traits. The relative pinnacle of such research was based on allozymic analysis. The goal of our project was to evaluate the level of hybridization in the main water bodies of the Czech Republic with the main focus on the detection of involved hybrid species, the level of such hybridization, and the phenotypic characterization of hybrid individuals. For that reason, it was sampled over 400 specimens giving a dataset of 381 individuals. Tissue samples were sampled for DNA isolation and each of the...
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Typing of bacterial populations based on methylation site detection
Hlavatá, Kristína ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
Táto bakalárska práca sa zameriava na detekciu metylácií DNA a vývoj metodiky typizácie bakteriálnych kmeňov. DNA metylácie hrajú kľúčovú úlohu ako regulačný mechanizmus v genóme, ktorý ovplyvňuje konečné vlastnosti organizmov. Použili sme DeepSignal2 na detekciu metylačných vzorov v 10 kmeňoch Klebsielly pneumoniae. Okrem toho sme navrhli metódu typizácie na základe identifikovaných metylácií pre kategorizáciu bakteriálnych kmeňov. Táto práca prispieva k zlepšeniu našeho chápania regulačných mechanizmov v bakteriálnych genómoch a predstavuje nový prístup k typizácii kmeňov pomocou vzorov metylácie DNA. Poskytuje cenné poznatky o charakterizácii a klasifikácii bakteriálnych kmeňov na základe ich metylómov.
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