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Development of Meta-Server for Prediction of Mutations Effects on Protein Function
Lisák, Peter ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This bachelor thesis deals with analysis of genomic data, more specifically prediction of effects of mutations on protein function using a protein sequence or tertiary structure. The theoretical introduction describes the basics of genetics and bioinformatics and is followed by description of selected prediction tools such as SIFT, MAPP and AUTO-MUTE. A unified interface for work with different tools is proposed in the thesis. The meta-server interface allows running a computation and collecting results from one site. meta-server combines results of implemented tools and provides a consensual prediction, which is expected to be more accurate than the results from individual tools. Finally, testing of meta-server on the real data and comparisons of predictions with the experimentally obtained results are presented.
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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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Gene Detection in DNA Sequences
Roubalík, Zbyněk ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
Gene detection in DNA sequences is one of the most difficult problems, which have been currently solved in bioinformatics. This thesis deals with gene detection in DNA sequences with methods using Hidden Markov Models. It contains a brief description of the fundamental principles of molecular biology, explains how genetic information is stored in DNA sequences, as well as the theoretical basis of the Hidden Markov Models. Further is described subsequent approach in the design of specific Hidden Markov Models for solving the problem of gene detection in DNA sequences. Is designed and implemented application, which uses previously designed Hidden Markov model for gene detection. This application is tested on the real data, results of these tests are discussed in the end of the thesis, as well as the possible extension and continuation of the project.
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Prediction of Transposons in DNA
Černohub, Jan ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
Cílem práce je seznámení se s problematikou uchovávání informace v DNA, provést rešerši na téma transpozony, bioinformatické nástroje a algoritmy, které jsou používány k jejich detekci v nasekvenovaných genomech a vytvořit tak stručný úvod do obsáhle problematiky, včetně jejího zasazení do kontextu současně probíhajícího výzkumu v dané oblasti. Na základě přehledu stávajících algoritmů a nástrojů pro detekci transpozonů je navržen a implementován nástroj pro hledání tzv. LTR transpozonů.
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DNA Fragmnent Assembly
Paulenda, Ján ; Jaša, Petr (referee) ; Burgetová, Ivana (advisor)
The main subject of this Bachelor's thesis is the DNA fragment assembly. The problem is transposed to finding a shortest superstring problem. Different assembly techniques and string aligning methods are introduced in the theoretical part. Programming language Perl, which was used to implement the assembly, is also widely mentioned, along with its features. Last part of the thesis involves tests' statistics of the final implemented solution.
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Clustering of Biological Sequences
Kubiš, Radim ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
One of the main reasons for protein clustering is prediction of structure, function and evolution. Many of current tools have disadvantage of high computational complexity due to all-to-all sequence alignment. If any tool works faster, it does not reach accuracy as other tools. Further disadvantage is processing on higher rate of similarity but homologous proteins can be similar with less identity. The process of clustering often ends when reach the condition which does not reflect sufficient quality of clusters. Master's thesis describes the design and implementation of new tool for clustering of protein sequences. New tool should not be computationally demanding but it should preserve required accuracy and produce better clusters. The thesis also describes testing of designed tool, evaluation of results and possibilities of its further development.
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Detection of Related Proteins with Modified Function
Hon, Jiří ; Bendl, Jaroslav (referee) ; Martínek, Tomáš (advisor)
Protein engineering is a young dynamic discipline with great amount of potential practical applications. However, its success is primarily based on perfect knowledge and usage of all existing information about protein function and structure. To achieve that, protein engineering is supported by plenty of bioinformatic tools and analysis. The goal of this project is to create a new tool for protein engineering that would enable researchers to identificate related proteins with modified function in still growing biological databases. The tool is designed as an automated workflow of existing bioinformatic analyses that leads to identification of proteins with the same type of enzymatic function, but with slightly modified properties - primarily in terms of selectivity, reaction speed and stability.
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Computational Methods for Annotation Analysis of Genetic Variations
Fülöp, Tibor ; Bendl, Jaroslav (referee) ; Martínek, Tomáš (advisor)
Analýza a interpretace variací DNA je důležité pro zkoumání genetického pozadí dědičnosti, nemocí a jiných fenotypových rysů. Tato práce stručně úvadí oblasti molekulární biologie a základních principů genetiky, popisuje metody pro anotační analýzy genetických variací, genomové asociační studie a metody pro analýzy obohacení s jejich implementací. V rámci této práce jsme představili nový webový nástroj Varanto, který může být použit k anotaci, vizualizaci a analýze genetických variací. Může být použit k analýze obohacení anotací pomocí hypergeometrického testu pro danou množinu variací. Varanto obsahuje uživatelské webové rozhraní vyvinuté pomocí frameworku Shiny jazyka R. Výkon a funkcionalita nástroje jsou testovány a demonstrovány podle výkonových benchmarků a na základě analýzy a interpretace dat z dříve publikovaných genomových asociačních studií.
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