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Methods of processing Oxford Nanopore sequencing data for metagenomics
Barilíková, Lujza ; Provazník, Ivo (referee) ; Kupková, Kristýna (advisor)
The revolutionary sequencing technology introduced by Oxford Nanopore Technologies – MinION holds a great promise in the field of metagenomics. Low cost, produced long reads and portability, due to its small dimensions, represents only one of the many advantages of this technology. Despite the benefits, there is a lack of available computational tools for handling the produced data. The theoretical part of the thesis first introduces current sequencing technologies with main focus on the third-generation sequencing and especially on nanopore sequencing. The recent possibilities of metagenomic data visualization are introduced. The main purpose of the bachelor thesis is to make an algorithm for binning of metagenomic samples based on use of dimensionality reduction techniques straight on raw data produced by nanopore sequencing.
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Gene identification in nanopore squiggles
Talanin, Nikita ; Nykrýnová, Markéta (referee) ; Bartoň, Vojtěch (advisor)
Nanopore sequencing is a new and rapidly developing technology that allows for the direct sequencing of single-stranded DNA and RNA in real-time. The result of the sequencing is the so-called squiggle, which is a time series of current intensities as nucleotides pass through the nanopore. Identifying genes in these squiggles is a crucial step for the utilization of this data in genomic studies. This bachelor's thesis focuses on the development and testing of a method for automatic gene identification in squiggles from nanopore sequencing. The aim was to create a system capable of quickly and accurately identifying genes in squiggles, thereby supporting further analysis and interpretation of nanopore sequencing data. The method utilizes Convolutional Neural Networks (CNN), which have been successfully used in many other areas of bioinformatics. A large dataset of squiggles, labeled according to the gene they represent, was used to train the model. The results show that the system can identify genes in squiggles with a certain level of accuracy and can be an effective tool for nanopore sequencing data analysis
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Gene identification in nanopore squiggles
Talanin, Nikita ; Nykrýnová, Markéta (referee) ; Bartoň, Vojtěch (advisor)
Nanopore sequencing is a new and rapidly developing technology that allows for the direct sequencing of single-stranded DNA and RNA in real-time. The result of the sequencing is the so-called squiggle, which is a time series of current intensities as nucleotides pass through the nanopore. Identifying genes in these squiggles is a crucial step for the utilization of this data in genomic studies. This bachelor's thesis focuses on the development and testing of a method for automatic gene identification in squiggles from nanopore sequencing. The aim was to create a system capable of quickly and accurately identifying genes in squiggles, thereby supporting further analysis and interpretation of nanopore sequencing data. The method utilizes Convolutional Neural Networks (CNN), which have been successfully used in many other areas of bioinformatics. A large dataset of squiggles, labeled according to the gene they represent, was used to train the model. The results show that the system can identify genes in squiggles with a certain level of accuracy and can be an effective tool for nanopore sequencing data analysis
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Advanced Computational Methods for Increasing the Discriminatory Power of Genotyping Methods
Nykrýnová, Markéta ; Budinská, Eva (referee) ; Hrabák,, Jaroslav (referee) ; Škutková, Helena (advisor)
Tato disertační práce je zaměřena na vytvoření nových výpočetních metod, které zvýší diskriminačních schopnost genotypizačních metod. Hlavní důraz je kladen na odlišení blízce příbuzných bakterií, které pocházejí například z jedné nemocnice či jednoho oddělení. V první části práce jsou popsány současné typizační metody a jsou představeny nové postupy pro identifikaci genetických markerů s vysokou mírou sekvenční variability, pomocí kterých lze lépe rozlišit bakteriální populaci. Navržené metody jsou založeny na výpočtu signálů entropie a analýze nenamapovaných čtení. Druhá část práce se zabývá návrhem nových metod zpracování surových dat z nanopórového sekvenování, které lze použít pro rychlou vysoce citlivou typizaci bakterií bez nutnosti převádět proudové signály na nukleotidové sekvence. Předložená práce přispívá ke zlepšení a zpřesnění rutinně používaných typizačních metod pomocí navržených bioinformatických postupů a představuje unikátní přístup využití doposud experimentální techniky nanopórového sekvenování pro rychlou genotypizaci a analýzu bakterií.
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Processing and analysis of the human lung microbiome from nanopore sequencing data
Molíková, Anna ; Bartoň, Vojtěch (referee) ; Nykrýnová, Markéta (advisor)
This bachelor’s thesis deals with processing and analysis of the human lung microbiome from nanopore sequencing data. Firstly this thesis introduces the lung microbiome and its composition in health and illness. Then it focuses on generations of sequencing technologies, mainly describing nanopore sequencing. The last chapter discusses different methods used for lung microbiome analysis. The practical part of this thesis preprocesses sequencing data, followed by their taxonomic analysis and the search for antibiotic resistance genes. From the obtained results, the composition of the lung microbiome in each of the processed samples is then evaluated.
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Evolutionary dynamics of satellite DNA in plant genomes
ÁVILA ROBLEDILLO, Laura
Satellite DNA (satDNA) belongs to the highly repetitive fraction of eukaryotic genomes. It is best characterized by the formation of long arrays of almost identical sequences that are tandemly repeated. These repeats are widely distributed in plant species where they can make up a substantial proportion of their genomes. Despite the long history of satDNA research, the classic methodology did not allow for its comprehensive characterization. Consequently, the fragmentary information gathered during the last 60 years does not answer the many questions surrounding the evolution of these elements. The development of new techniques in sequencing, together with the availability of new bioinformatics tools for analyzing different genome fractions, has presented an opportunity to advance studies of tandem repeats. This thesis describes the landscape characterization of satDNA in the genome of Fabeae species by exploring the diversity of satDNA within a genome, the association of these elements with functional centromeres, as well as their genome-wide organization. We employed new computational pipelines specifically designed for the analysis of tandem repeats from next generation sequencing data, and combined their results with molecular and cytogenetic methods to achieve comprehensive characterization of the satellite repeats.
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Mechanisms and aplications of macromolecule translocation across membranes of eukaryotic cells by bacterial toxins
Poledňák, Jan ; Fišer, Radovan (advisor) ; Žáčková Suchanová, Jiřina (referee)
Toxin translocation across the cytoplasmic membrane of the eukaryotic cell is a potent virulence factor of bacteria causing disease to eukaryotic organisms. Toxins translocate their domains responsible for the toxic activity inside the cell or create pores in cell membrane allowing the transmembrane traffic of ions, DNA, RNA or proteins. Knowledge of the toxin translocation process enables to characterize the mechanism and also the properties of the pore-forming toxin. Some of these toxins have been described in such a detail that were changed using site-directed mutagenesis and can serve as tools for characterization of the translocated molecules. One of such examples is the transfer of nucleotides or the whole nucleic acid molecules across the membrane through the pore of S. aureus α-hemolysine. Nowadays, this application is commercially used for DNA sequencing. Keywords: translocation, bacterial toxins, plasmatic membrane, nanopore sequencing
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Methods Of Processing Oxford Nanopore Sequencing
Data For Metagenomics
Barilíková, Lujza
The presented paper describes a new method of processing data produced by revolutionary sequencing technology introduced by Oxford Nanopore Technologies – MinION, which holds a great promise in the field of metagenomics. Low cost, produced long reads and portability, due to its small dimensions, represents only one of the many advantages of this technology. Despite of the benefits, there is a lack of available computational tools for handling the produced data and that is the reason, why a new method of processing such data should be created. In this study such method is created based on dimensionality reduction for data visualization.
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Methods of processing Oxford Nanopore sequencing data for metagenomics
Barilíková, Lujza ; Provazník, Ivo (referee) ; Kupková, Kristýna (advisor)
The revolutionary sequencing technology introduced by Oxford Nanopore Technologies – MinION holds a great promise in the field of metagenomics. Low cost, produced long reads and portability, due to its small dimensions, represents only one of the many advantages of this technology. Despite the benefits, there is a lack of available computational tools for handling the produced data. The theoretical part of the thesis first introduces current sequencing technologies with main focus on the third-generation sequencing and especially on nanopore sequencing. The recent possibilities of metagenomic data visualization are introduced. The main purpose of the bachelor thesis is to make an algorithm for binning of metagenomic samples based on use of dimensionality reduction techniques straight on raw data produced by nanopore sequencing.
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Mechanisms and aplications of macromolecule translocation across membranes of eukaryotic cells by bacterial toxins
Poledňák, Jan ; Fišer, Radovan (advisor) ; Žáčková Suchanová, Jiřina (referee)
Toxin translocation across the cytoplasmic membrane of the eukaryotic cell is a potent virulence factor of bacteria causing disease to eukaryotic organisms. Toxins translocate their domains responsible for the toxic activity inside the cell or create pores in cell membrane allowing the transmembrane traffic of ions, DNA, RNA or proteins. Knowledge of the toxin translocation process enables to characterize the mechanism and also the properties of the pore-forming toxin. Some of these toxins have been described in such a detail that were changed using site-directed mutagenesis and can serve as tools for characterization of the translocated molecules. One of such examples is the transfer of nucleotides or the whole nucleic acid molecules across the membrane through the pore of S. aureus α-hemolysine. Nowadays, this application is commercially used for DNA sequencing. Keywords: translocation, bacterial toxins, plasmatic membrane, nanopore sequencing
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