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Current genomic and cytogenomic methods in analysis of chromosome rearrangements
Buryšová, Sára ; Sember, Alexandr (advisor) ; Mandáková, Terezie (referee)
Chromosome rearrangements represent one of the major mechanisms driving the eukaryotic genome evolution. They may significantly contribute to reproductive isolation and diversification, including the evolution of complex life-history traits linked e.g. with local adaptation. They are structural changes leading to alteration in the morphology and/or number of chromosomes, which can have a direct effect on the evolution of genes and their expression profiles, the frequency and distribution of recombination in the genome, and the functional dynamics of processes operating in the interphase nucleus. However, they may be also causal for etiology (or a consequence) of inherent diseases and tumorigenesis. The study of chromosome rearrangements and the mechanisms of their emergence is related to the identification and characterization of rearrangement breakpoints (i.e. where double-strand break occurred and chromosome segments subsequently rejoined). One possibility is to analyze chromosomes and interspecific changes in the arrangement of linkage groups/synteny blocks using cytogenetic and cytogenomic methods (e.g. cross-species mapping of whole-chromosome hybridization probes). More detailed insight is provided by comparative genomics, nowadays mainly represented by so-called third-generation methods (the...
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Current approaches to whole genome sequencing and de novo genome assembly
Halenková, Zuzana ; Reifová, Radka (advisor) ; Röslein, Jan (referee)
The cost of sequencing has fallen almost ten thousand times over the past ten years due to the development of second and third generation sequencers. Sequencing and assembling the whole genome sequence of an organism is thus becoming a more affordable tool which can be utilized in many fields of science. On the way to the complete DNA sequence of an organism, multiple important decisions have to be made. These are crucial for the successful assembly of high- quality whole genome sequence and regard sample preparation, choice of sequencing technique and choice of an appropriate approach to whole genome assembly. This bachelor thesis describes various methods which can be utilized in individual steps of the process and aspects to consider while making the decisions. Keywords: next generation sequencing, third generation sequencing, whole genome sequencing, de novo assembly, genome assembly algorithms
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Current approaches to whole genome sequencing and de novo genome assembly
Halenková, Zuzana ; Reifová, Radka (advisor) ; Röslein, Jan (referee)
The cost of sequencing has fallen almost ten thousand times over the past ten years due to the development of second and third generation sequencers. Sequencing and assembling the whole genome sequence of an organism is thus becoming a more affordable tool which can be utilized in many fields of science. On the way to the complete DNA sequence of an organism, multiple important decisions have to be made. These are crucial for the successful assembly of high- quality whole genome sequence and regard sample preparation, choice of sequencing technique and choice of an appropriate approach to whole genome assembly. This bachelor thesis describes various methods which can be utilized in individual steps of the process and aspects to consider while making the decisions. Keywords: next generation sequencing, third generation sequencing, whole genome sequencing, de novo assembly, genome assembly algorithms
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