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A tool for prediction of small RNA in RNA-Seq data
Pomykalová, Barbora ; Čejková, Darina (referee) ; Jurečková, Kateřina (advisor)
This diploma thesis focuses on the detection of small RNA (sRNA) in the bacterial genome. sRNAs are short non-coding transcripts that play a key role in gene expression. To date, there are several algorithms focusing on the detection of sRNAs from RNA-Sequencing (RNA-Seq) data that can be obtained by some of the sequencing platforms. The most frequently used platforms are Illumina and Ion Torrent belonging to the next generation sequencing and PacBio with Oxford Nanopore belonging to the third generation of sequencing. In this work, the workflow of sRNA detection using freely available tools was described and then an own unique tool for sRNA detection – the SEARCHsRNA tool – was designed. Two open-source software tools – Rockhopper and DETR'PROK, together with newly created tool, were tested on RNA-Seq data for bacteria Vibrio atlanticus LGP32.
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Analysis of horizontal transfer of genetic components using static network analysis
Labanava, Anastasiya ; Jurečková, Kateřina (referee) ; Schwarzerová, Jana (advisor)
The bachelor's thesis focuses on the issue of horizontal genetic elements transfer between bacteria of different strains and the software analysis implementation that enables horizontally transferred genes identification. The packages and tools used were tested on a dataset of bacterial genomes from several strains. The thesis’ theoretical part provides a detailed description of the genetic components transfer between bacteria and describes modern laboratory techniques that enable genome sequencing in various ways. In the practical part, the thesis deals with the preprocessing of genomic files to obtain suitable data for annotation. To detect the horizontal transfer of genetic elements between bacteria, a script is introduced, which organizes annotated bacteria to tables and searches for the same genes in their genomes that, under theoretical assumptions, were horizontally transferred. Furthermore, the gene transfer is visualized using tools that graphically represent phylogenetic relations between bacteria. In the final step, bacterial genomes are connected into networks, and based on their static analysis, a discussion is conducted on the results accuracy and the success of the proposed analysis.
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Identification of non-coding RNAs of Clostridium beijerinckii NRRL B-598 using RNA-Seq data
Pomykalová, Barbora ; Sedlář, Karel (referee) ; Jurečková, Kateřina (advisor)
This bachelor thesis contains short introduction into bacterial small non-coding RNA problematic. It is oriented on their features and functions in organisms, especially in bacteria Clostridium beijerinckii NRRL B-598. Bachelor thesis also contains description of various laboratory methods for gene expression determination and suggests a detection method for small non-coding RNA in bacteria Clostridium beijerinckii NRRL B-598. Suggested method works with data, which were obtained by RNA-Seq technology. Within the framework of the bachelor thesis was suggested method implemented in programming and numeric computing platform MATLAB and its results were discussed.
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Methods for prediction of RNA secondary structure
Polzerová, Nikola ; Musilová, Jana (referee) ; Jurečková, Kateřina (advisor)
This bachelor thesis discuss RNA secondary structure and it’s prediction in particular. It describes various secondary structure elements and presents some secondary structure prediction methods. Within the framework of bachelor thesis, three computational methods for secondary structure prediction were implemented in programming and numeric computing platform MATLAB. These methods are Nussinov algorithm, Zuker algorithm and Crumple method. Implemented algorithms approched the prediction in terms of base pair maximalization or free energy minimalization. Their function was verified on the created dataset and the results were compared with known secondary structures.
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Detection of chimeras in amplicon sequencing
Heřmánková, Kristýna ; Jurečková, Kateřina (referee) ; Sedlář, Karel (advisor)
Chimeric sequences are the most common artifacts that can occur in sequencing data after the sample amplification using the polymerase chain reaction. The presence of these artifacts can negatively affect results of the analysis. Therefore, the detection and subsequent filtration of chimeric sequences is an important step in the computational processing of sequencing data. This work deals with the principle of chimera formation and the possibility of reducing their occurrence. The aim of this work is to implement an algorithm for chimeras detection in R language and testing its accuracy on data provided by the Veterinary Research Institute in Brno.
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Gene regulation in Clostridium beijerinckii NRRL B-598
Schwarzerová, Jana ; Jurečková, Kateřina (referee) ; Sedlář, Karel (advisor)
Diplomová práce se zabývá studiem genové regulace v Clostridium beijerinckii NRRL B-598, pro následné odvození genové regulační sítě bakterie C. beijerinckii NRRL B-598. V teoretické části této práce je uvedena obecná nomenklatura problematiky genové regulace se zaměřením na nomenklaturu genových regulačních sítí. Následně jsou zde popsané laboratorní metody, sloužící pro získání vhodných dat popisující expresi genů. Tato data jsou základem pro studium genové regulace a návrhy genových regulačních sítí. Práce se zaměřuje především na technologii RNA-Seq a stručný popis laboratorních dat získaných ze zmíněné bakterie C. beijerinckii NRRL B-598. V praktické části se práce zabývá předzpracováním těchto surových laboratorních dat a následným studiem genové regulace se zaměřením na odvození operonů a vytvoření prvních genových regulačních sítí pomocí různých přístupů pro C. beijerinckii NRRL B-598.
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User interface for data extraction from GenBank data format
Jurečková, Kateřina ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis contains a literature review on the topic of the GenBank database, its most used flat file format gbk and its comparison with other formats of sequential data. Furthermore this thesis describes the structure of mitochondrial DNA of animals and plants and plastid DNA of plants. In the practical part of this thesis is evaluation of successful automatic data extraction from GenBank flat file format from whole mitochondrial sequences by genbankread function in Matlab. And it describes also a new application for GenBank data extraction. In the end this application is used in analyses of mitochondrial genomes.
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Operon structures inference in genome-wide analysis
Nejezchlebová, Julie ; Jurečková, Kateřina (referee) ; Schwarzerová, Jana (advisor)
The bachelor thesis is devoted to the problem of derivation of operon structures and creation of a software tool that allows prediction of operon structures. The tool both predicts operons based on gene expression information, but also refines already predicted operons with gene expression information. The tool is tested on the bacteria Escherichia coli BW25113 and Clostridium beijerinckii NRRL B-598. The theoretical part is devoted to description of operon structure and function, genome sequencing, transcriptome analysis, Clostridium beijerinckii NRRL B-598, Escherichia coli BW25113 and already available online tools for inferring operon structures. In the practical part of the thesis, the pre-processing of raw transcriptomic data to obtain a suitable format for the prediction of operon structures, testing of online tools and the actual implementation of the tool itself are discussed.
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Correlates finding of heart rate changes in fMRI data
Jurečková, Kateřina ; Gajdoš, Martin (referee) ; Bartoň, Marek (advisor)
This master’s thesis deals with problematic of correlates finding of heart rate changes in fMRI data. The first part describes principle of fMRI, creation of BOLD signal, data acquisition, their pre-processing and analysis. The next part describes heart rate variability and its impact on fMRI data. The following section is dedicated to pre-processing of heart rate time series to the form, which can be used in correlates finding of heart rate variability and fMRI data with generalized linear model. The process of statistical testing and its result with discussion can be found in the last part of this thesis.
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Online Database of Bacterial Sequence and Melt Types
Františová, Zuzana ; Jurečková, Kateřina (referee) ; Sedlář, Karel (advisor)
Předmětem této diplomové práce je vytvoření databáze známých sekvenčních a melt typů patogenních bakterií a nástroje pro správu databáze. Metoda popisovaná v této práci je poměrně nová technika typizace patogenních bakterií založena na překladu sekvenčních typů na příslušející melt typ a využívá k tomu převodní klíč, který byl vytvořen ve spolupráci s Centrem molekulární biologie a genové terapie Interní hematologické a onkologické kliniky Fakultní nemocnice Brno. Obsahem práce je vytvoření prostoru na databázovém serveru, načtení potřebných dat, aplikace převodního klíče, vytvoření GUI, vytvoření dalších vhodných ošetření a rozšíření, testování a následná analýza výsledků. V první kapitole jsou diskutovány nejznámější metody bakteriální typizace, další kapitola je pak věnována server-client aplikacím a databázovým nástrojům. Třetí kapitola popisuje implementaci databáze na server a čtvrtá kapitola stručně shrnuje všechny funkce programu. V poslední kapitole je pak popsána analýza vylepšení převodního klíče, které získalo pracovní název půlené alely.
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