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DNA Sequence Classification
Heczková, Petra ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
The work deals with DNA sequence classification. The first part summarizes information about existing methods a their characteristics. In the second part there are description of implementation and experiments. Average sensitivity of method was 65% and specificity 92%.
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Clustering of Protein Sequences Based on Primary Structure of Proteins
Jurásek, Petr ; Stryka, Lukáš (referee) ; Burgetová, Ivana (advisor)
This master's thesis consider clustering of protein sequences based on primary structure of proteins. Studies the protein sequences from they primary structure. Describes methods for similarities in the amino acid sequences of proteins, cluster analysis and clustering algorithms. This thesis presents concept of distance function based on similarity of protein sequences and implements clustering algorithms ANGES, k-means, k-medoids in Python programming language.
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Techniques for Comparing Biological Sequences
Sladký, Roman ; Křivka, Zbyněk (referee) ; Burgetová, Ivana (advisor)
This work presents the building up of basic biological units DNA, RNA and proteins as well as their function. Provided data are kept in biological databases which are connected worldwide to supply preferable communication along with all kinds of available information to be used in the scientific research. The secret of alive is hidden in genes coded in sequences of nucleotides. Genes enable the creation of proteins which are made of sequences of amino-acids. The wide-spread methods of comparing these sequences are FASTA and BLAST algorithms. Their base is used for the PSProt program which is described in this work. PSProt program is the tool for comparing the sequences of proteins. First it is necessary to synthesise the protein from the DNA oligonucleotide because it codes the surveyed protein. The most similar proteins are searched out by heuristic of hitpoints, then their final score that is essential for aligning is modified by semiglobal alignment algorithm.
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Gene Searching - Web Application
Stiborová, Lucie ; Koutný, Jiří (referee) ; Burgetová, Ivana (advisor)
The aim of my Bachelor's Thesis is to create a user interface and to implement the web application with the genes' searching. This is the educational application when each user has a possibility of entering own nucleotide sequences or selecting a redefined chain. This application has to be able to read, process and decide on the existence of a potential gene. On the base of this simple statistic method the result is given back to the user.
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Gene Detection in DNA Sequences
Bahurek, Tomáš ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
This work is about gene detection in DNA sequencies. It explains how the information in DNA is stored, shows preview of various gene prediction methods, describes picked methods and results of testing those methods on real data (genome of bacteria E. Coli K12), compares efficiency of methods with various paramaters and efficiency between methods.
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Database System for Biological Data Management
Drlík, Radovan ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This thesis describes the problems of storage and management of biological data, particularly of Haloalkane Dehalogenase enzymes. Furthermore, the thesis aims at project HADES (HAloalkane DEhalogenase databaSe) initiated by protein engineering group of Loschmidt Laboratories, Masaryk University in Brno. This is a project whose main goal is simply to store, preserve and display a wide variety of proteins data. The result of this work is a flexible database system allowing easy extensibility and maintainability, which is built on technologies Apache, PostgreSQL and PHP using the Zend Framework.
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Molecular and Genomic Methods for Analyzing Hybridization in Aspergillus and other Fungi
Jirkovský, Pavel ; Sklenář, František (advisor) ; Kolařík, Miroslav (referee)
Interpecies hybridization is being studied since the first half of 20. century, when it was described based on phenotypical traits on plant model. Study of this process was historically centred around botanical studies, while its importance in mycology is just being uncovered in recent years. Introgression is a phenomenon that can occur when hybrid backcrosses with one of the parental species. Based on recent studies it is apparent that hybridization played its role in evolution of MAT locus genes of Neurospora, transfer of adaptive traits with Ophiostoma species (invasive pathogen of elm trees). Within Aspergillus family hybridization was described both on intraspecific and interspecific level. More detailed study of this process and improving of used methods could potentially help in clinical application by uncovering adaptive genes responsible for resistance towards antimycotics, higher virulence and other traits.
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Cell Biology in Czech Lower-secondary Biology Textbooks
Zupko, Jakub ; Dvořáková, Radka (advisor) ; Kuba, Radim (referee)
Cell biology is a dynamic but also complex and abstract scientific field. Therefore, it is crucial that teachers have sufficient quality teaching material to teach it. This paper aims to assess the quality of the cell biology chapters in five Czech textbooks for 6th-grade science. Specifically, the textbooks of Fraus, Nová Škola, Prodos, SPN and Taktik publishers are the set under study. The content analysis of the textbooks focuses on six aspects: scope of the material, terminology, difficulty of the explanatory text (measured by the Hrabí method), content accuracy, the cognitive difficulty of the accompanying tasks (according to Bloom's taxonomy) and the nature of the non- verbal component of the textbooks. Differences were found in the didactic equipment and the correctness of the content of individual textbooks. In four of the five explanatory texts it is possible to find incorrect information (at least three and at most twelve false statements). Most of the accompanying tasks are aimed at the lowest levels of Bloom's taxonomy. The nonverbal component on average occupies almost one-third of the page space, with the most common type of pictorial component being a sketch. The most suitable textbook, based on the examined criteria, is the textbook published by SPN, followed by the textbook...
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Ecology of yeasts in forest soils
Mašínová, Tereza ; Baldrian, Petr (advisor) ; Marečková, Markéta (referee) ; Kolařík, Miroslav (referee)
Microbial communities inhabiting upper soil horizons represent an important component of forest ecosystems. However, despite the evidence that yeasts represent an integral part of topsoil fungal communities, their role in forest ecosystems received so far little attention. The aims of my PhD thesis were to describe yeast communities in soil and litter of a temperate forest using high- throughput sequencing of environmental DNA, identify dominant yeast species and to explore how the composition of yeast communities reflects the biotic and abiotic factors of the environment. I also aimed to isolate yeasts from forest topsoil, describe novel yeast taxa abundant according to the environmental DNA survey and screen representative isolates for the traits relevant to their involvement in organic matter transformation. I have demonstrated that in forest topsoil, yeasts represent a substantial proportion of fungal communities with higher relative abundance in soil than in litter. In litter, yeast communities differ significantly among beech, oak and spruce-dominated stands. Drivers of community assembly are probably more complex in soils and comprise the effects of soil chemistry and vegetation. Even though there are similarities in the response of the communities of yeasts and filamentous fungi to...
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