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Web Application for Primer Selection for 16S rRNA Amplicon Sequencing
Jurča, Jan ; Martínek, Tomáš (referee) ; Smatana, Stanislav (advisor)
Main goal of this thesis was an implementation of web application, that can evalutate and recommend primer pairs for 16S rRNA amplicon sequencing, according to users specific needs and by this simplify the procces of primer pair selection. Primer pair evaluation is based on database of primer pairs, which contains data about senzitivity and specifity of each primer pair. Part of the work was also the performance optimization of the primer pair analysis algorithm, that computes senzitivity and specifity data. This optimization helped in an integration of algorithm into the application, which means that users can submit their own primer pair sequences, run analysis and get informations about position of amplified region, sensitivity and specifity.
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Analysis of the dicyemid diversity using amplicon sequencing
FLEGROVÁ, Tereza
Using amplicon sequencing, this study reveals dicyemid diversity around the world as well as within individual cephalopod hosts. A wide number of samples of multiple species were collected to reflect true dicyemid diversity. Heterogeneity primers were designed in order to improve the sequencing performance of the Illumina platform. A complex bioinformatic pipeline was implemented to process non-overlapping reads. The species delimitation methods were used to categorize occurring dicyemid types. Using the output of implemented methods, dicyemid diversity was assessed, proposing new trends opposing the current methodology.
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Vliv potravní preference všenek (Phthiraptera: Amblycera) na formování jejich mikrobiomů
ŽIŽKOVÁ, Kateřina
Microbiome diversity of chewing lice belongs to generaly unexplored topics. This thesis provides the first insight into the microbiomes of 15 chewing lice species of the genus Menacanthus. We detected the presence of two dominant symbiotic bacteria, which occurred in almost all species. We also compared the microbiome diversity of lice with different diet preferences (blood feeding and feather feeding species). Based on these analyses, we identified the main determinants shaping the microbiomes of Menacanthus lice. The microbiomes are namely affected by Menacanthus species identity, its geographical origin, dietary niche, and the extent of the host spectrum that the lice parasitize.
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Web Application for Primer Selection for 16S rRNA Amplicon Sequencing
Jurča, Jan ; Martínek, Tomáš (referee) ; Smatana, Stanislav (advisor)
Main goal of this thesis was an implementation of web application, that can evalutate and recommend primer pairs for 16S rRNA amplicon sequencing, according to users specific needs and by this simplify the procces of primer pair selection. Primer pair evaluation is based on database of primer pairs, which contains data about senzitivity and specifity of each primer pair. Part of the work was also the performance optimization of the primer pair analysis algorithm, that computes senzitivity and specifity data. This optimization helped in an integration of algorithm into the application, which means that users can submit their own primer pair sequences, run analysis and get informations about position of amplified region, sensitivity and specifity.
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