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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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Mobile genetic elements detection by genomic signal processing
Nováková, Jarmila ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
Mobile genetic elements are occupied by this project. It is aimed at their features, which can be used for their detection. It also deals with issue of conversion of symbolic sequence into numerical form. Classifications of mobile genetic elements are explained, basic types of mobile genetic sequences are described, and principles of numerical maps and detection in symbolic represetation are also clarified. Conversion of symbolic genetical sequences by chosen numerical map and calculation of normalized correlation values for set of mobile genetic elements are compiled. Analysis of the mobile genetic elements properties is performed for design of detector. The library of themes is created at the end for usage by designed detector.
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Analýza vybraných W obohacených repetic u předivky brslenové \kur{Yponomeuta cagnagella} (Lepidoptera)
PILÍKOVÁ, Aneta
This thesis focuses on the repetitive sequences located in the W chromosome of the spindle ermine moth (Yponomeuta cagnagella) (Lepidoptera). The copy number of the selected repeats was established in male and female genomes from two geographic populations using real-time PCR (qPCR). Fluorescence in situ hybridization (FISH) was used to localize these sequences in female pachytene nuclei. The satellite tandem repeat and the transposon Maverick are present in the W chromosome in high copy numbers. In contrast to previously conducted bioinformatical analyses, the rDNA cluster is probably localized in an autosome in Y. cagnagella. The Maverick transposon was detected in both extensive terminal regions of the W chromosome.
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Mobile genetic elements detection by genomic signal processing
Nováková, Jarmila ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
Mobile genetic elements are occupied by this project. It is aimed at their features, which can be used for their detection. It also deals with issue of conversion of symbolic sequence into numerical form. Classifications of mobile genetic elements are explained, basic types of mobile genetic sequences are described, and principles of numerical maps and detection in symbolic represetation are also clarified. Conversion of symbolic genetical sequences by chosen numerical map and calculation of normalized correlation values for set of mobile genetic elements are compiled. Analysis of the mobile genetic elements properties is performed for design of detector. The library of themes is created at the end for usage by designed detector.
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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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