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Pozitive and negative selection of mitochondrial genome
Svoboda, Matěj ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis deals with positive and negative selection detection in mitochondrial genome of invertebrates and vertebrates. The component of this paper is to interpret the theory of evolution and evolution models. The main objective of this bachelor thesis is to formulate the algorithm package for a positive and negative selection detection in a program environment, RStudio. Consequently, outcomes of algorithm are compared to values acquired by tool PAML.
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Analysis of animal mitochondrial genes for DNA barcoding
Brabencová, Klára ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
The aim of this work is a literature review on the topic of the mitochondrial genome and DNA barcoding, building a dataset of mitochondrial sequences from GenBank database and creatione of a software function for extraction of individual genes that are present in the mitochondrial genome. This function was developed in Matlab. DNA barcoding is a method that uses short DNA sequence of mitochondrial genome for identification of species. There is no comprehensive work examining the appropriateness of different mitochondrial genes. This aim investigates the potential of other mitochondrial genes and evaluate their effectiveness for DNA barcoding and calculation of intra-and interspecific variability.
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Pozitive and negative selection of mitochondrial genome
Svoboda, Matěj ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis deals with positive and negative selection detection in mitochondrial genome of invertebrates and vertebrates. The component of this paper is to interpret the theory of evolution and evolution models. The main objective of this bachelor thesis is to formulate the algorithm package for a positive and negative selection detection in a program environment, RStudio. Consequently, outcomes of algorithm are compared to values acquired by tool PAML.
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Analysis of animal mitochondrial genes for DNA barcoding
Brabencová, Klára ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
The aim of this work is a literature review on the topic of the mitochondrial genome and DNA barcoding, building a dataset of mitochondrial sequences from GenBank database and creatione of a software function for extraction of individual genes that are present in the mitochondrial genome. This function was developed in Matlab. DNA barcoding is a method that uses short DNA sequence of mitochondrial genome for identification of species. There is no comprehensive work examining the appropriateness of different mitochondrial genes. This aim investigates the potential of other mitochondrial genes and evaluate their effectiveness for DNA barcoding and calculation of intra-and interspecific variability.
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Molecular analysis of the mitochondrial genom of \kur{Diuraphis noxia} (Aphididae)
CHUNDELOVÁ, Daniela
The complete sequence of mitochondrial DNA from Diuraphis noxia was obtained and characterized. The mitogenome contains a standard set of 13 protein-coding genes, 19 tRNA genes, 2 ribosomal RNA genes. A+T-rich and ?repets? regions in the same order as those of the other analyzed aphids. Comparison to mtDNAs from other Sternorrhyncha species obtained from GenBank revealed possible markers for studies on population differentiation. Phylogenetic analysis using parsimony and maximum likelihood confirmed the classification of Diuraphis noxia into the Aphididae.
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