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Analysis of NGS data for study of transposon activity in cancer cells
Hrazdilová, Ivana ; Čegan,, Radim (referee) ; Eduard, Kejnovský (advisor)
Theoretical part of this diploma thesis gives a brief characteristic of human mobile elements (transposons), which represents nearly 50% of human genome. It provides basic transposon clasification and describes types of transposons present in hunam genome, as well as mobilization, activation and regulation mechanisms. The work also deals with the domestication of transposons, describes the ways in which TE contribute to DNA damage and summarizes the diseases caused by mutagenic activity of transposons in the human genome. Conclusion of theoretical part describes next-generation sequencing technologies (NGS). As practical part, data from RNA-seq experimet were analyzed in order to compare differen transposon activity in normal and cancer cells from prostate and colorectal tissues. As like as publicly available sophisticated tools (TopHat), new scripts were created to analyze these data. The results show that cancer cells exhibit overexpression of transposons. This corresponds with the published results and suggests a connection of transposon activation with cancer development.
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Visualization of Transposons' Genomic Features
Nétková, Barbora ; Bendl, Jaroslav (referee) ; Vogel, Ivan (advisor)
This thesis deals with visualization of transposons' genomic features. The Genomic feature format (GFF) is an input file to visualisation. This type of file has strict definition and it is nowadays a de-facto standard format for genome description. Although there are several tools for GFF visualization, an open source application with advanced visualization features is missing. This work presents a design of such a tool. The application has a graphical user interface to simplify the user's work and combines the advantages of existing commercial products with free access. The application provides simple way to import user's biological data from a GFF file, creates hierarchical tree of individual elements including a detailed internal structure visualization in a subwindow.
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Eucaryotic Genomes Comparison
Puterová, Janka ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
Main motive of this master thesis was the need of good bioinformatics tools for genome comparison and improvement of one of the existing tools - RepeatExplorer. This work offers an overview of transposable elements in DNA, existing tools for identification and analysis of repetitions in sequenced genomes, summary of currently used genome sequencing methods. This work describes shortcomings of RepeatExplorer tool with focus on comparative analysis of genomes. Two solutions to remove these problems were designed and implemented. The first solution is designed for comparing pairs of genomes. The principle of this solution is based on comparison of similarity of distribution of contigs coverages using Kolmogorov-Smirnov test, thanks to which we are able to determine different parts in the genomes.The second solution, which is used to compare multiple genomes, is based on the method of mapping reads from compared genomes to the reference genome contigs and provides contigs coverage graphs, by which we are able to determine the variability of the repeats.Their functionality was verified on real NGS data of organism Silene latifolia.
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Eucaryotic Genomes Comparison
Puterová, Janka ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
Main motive of this master thesis was the need of good bioinformatics tools for genome comparison and improvement of one of the existing tools - RepeatExplorer. This work offers an overview of transposable elements in DNA, existing tools for identification and analysis of repetitions in sequenced genomes, summary of currently used genome sequencing methods. This work describes shortcomings of RepeatExplorer tool with focus on comparative analysis of genomes. Two solutions to remove these problems were designed and implemented. The first solution is designed for comparing pairs of genomes. The principle of this solution is based on comparison of similarity of distribution of contigs coverages using Kolmogorov-Smirnov test, thanks to which we are able to determine different parts in the genomes.The second solution, which is used to compare multiple genomes, is based on the method of mapping reads from compared genomes to the reference genome contigs and provides contigs coverage graphs, by which we are able to determine the variability of the repeats.Their functionality was verified on real NGS data of organism Silene latifolia.
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Visualization of Transposons' Genomic Features
Nétková, Barbora ; Bendl, Jaroslav (referee) ; Vogel, Ivan (advisor)
This thesis deals with visualization of transposons' genomic features. The Genomic feature format (GFF) is an input file to visualisation. This type of file has strict definition and it is nowadays a de-facto standard format for genome description. Although there are several tools for GFF visualization, an open source application with advanced visualization features is missing. This work presents a design of such a tool. The application has a graphical user interface to simplify the user's work and combines the advantages of existing commercial products with free access. The application provides simple way to import user's biological data from a GFF file, creates hierarchical tree of individual elements including a detailed internal structure visualization in a subwindow.
|
|
|
Analysis of NGS data for study of transposon activity in cancer cells
Hrazdilová, Ivana ; Čegan,, Radim (referee) ; Eduard, Kejnovský (advisor)
Theoretical part of this diploma thesis gives a brief characteristic of human mobile elements (transposons), which represents nearly 50% of human genome. It provides basic transposon clasification and describes types of transposons present in hunam genome, as well as mobilization, activation and regulation mechanisms. The work also deals with the domestication of transposons, describes the ways in which TE contribute to DNA damage and summarizes the diseases caused by mutagenic activity of transposons in the human genome. Conclusion of theoretical part describes next-generation sequencing technologies (NGS). As practical part, data from RNA-seq experimet were analyzed in order to compare differen transposon activity in normal and cancer cells from prostate and colorectal tissues. As like as publicly available sophisticated tools (TopHat), new scripts were created to analyze these data. The results show that cancer cells exhibit overexpression of transposons. This corresponds with the published results and suggests a connection of transposon activation with cancer development.
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