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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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RNA secondary structure prediction
Polzerová, Nikola ; Schwarzerová, Jana (referee) ; Jurečková, Kateřina (advisor)
Sekundární struktura RNA se stala v posledních letech fenoménem. Hraje klíčovou roli v pochopení principů genové exprese a stability RNA, a také pokládá důležitý základ pro správnou predikci terciálních struktur. Proto dochází k velice rychlému rozvoji predikce pomocí výpočetních metod a také pomocí metod strojového učení. V rámci práce byly popsány nejčastěji citované metody strojového učení pro predikci sekundárních struktur RNA. Na základě získaných znalostí byla implementována reziduální neuronová síť. Implementovaná reziduální síť byla netrénována, validována a otestována na sekvencích z datasetu bpRNA-1m, jejichž sekundární struktury neobsahují pseudouzly.
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Novel hepatitis C virus proteins
Zeman, Jakub ; Vopálenský, Václav (advisor) ; Horníková, Lenka (referee)
The hepatitis C virus (HCV) is a major etiological agent of chronic liver diseases. More than 170 million people worldwide are chronically infected, and more than 100 thousand of them develop hepatocellular carcinoma a year. HCV is an enveloped, positive-sense single-stranded RNA virus (+ssRNA virus) of the family Flaviviridae. Its genome is translated to produce a single polyprotein precursor that is further processed by cellular and viral proteases to form 10 viral proteins. Moreover, there is another protein encoded in an alternative reading frame. Two alternative translation mechanisms have been proposed for expression of this alternative reading frame protein (ARFP): a frameshift mechanism and translation initiating from internal start codons. Despite ten years of research its role in vivo is not yet explained. It appears that secondary structures in the core encoding region of HCV genome but not ARFP expression are required for robust viral translation and replication. The results of recent studies suggest that mutations distorting these structures may result not only in slowing down the viral cycle but also in a brand new and utterly unusual serological profile in patients as well as an increased level of expression of ARFP.
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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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RNA secondary structure prediction
Hadwigerová, Michaela ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Since the time RNA has been discovered by the nature scientist Miescher the structure and function of it has been forgotten for a long time. The prime role in science had always DNA. An increase of interest in RNA came with the discovery of the tRNA structure and its catalytic and enzymatic properties. These discoveries led to a great development wave of bioinformatics and structure and function analysis of RNA.
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The influence of intron sequences on splicing effectivity in Saccharomyces cerevisiae
Oplová, Michaela ; Půta, František (advisor) ; Malcová, Ivana (referee)
Pre-mRNA splicing is a highly regulated cellular process. The tight cooperation of spliceosome and other splicing factors that enable pre-mRNA cis-elements interpretation results in precise pre-mRNA splicing regulation. Short conserved splicing sequences within introns represent an elementary and indispensable element for intron removal from primary transcript, yet they are not sufficient signals for efficient splicing events. Additional pre-mRNA features affect complex splicing regulation. We took advantage of strains with slightly disrupted spliceosome (prp45(1-169)) to study the effect of ACT1 and MAF1 intronic sequences on splicing efficiency. Here we show, that ACT1 intron region between branch point (BP) and 3' splice site (3'ss) maintains splicing efficiency in mutant cells. However, the specific element within this region was not determined. In addition, results implicate an alternative BP in splicing efficiency modulation in yeast Saccharomyces cerevisiae. Interestingly, this alternative BP is localized in ACT1 intron outside of the BP-3'ss region. Furthermore, splicing factors with potential influence on 3'ss selection were studied. Heterodimer composed of Slu7p and Prp18p participates in 3'ss positioning to the active site of the spliceosome. Splicing analysis of substrates with two...
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Novel hepatitis C virus proteins
Zeman, Jakub ; Vopálenský, Václav (advisor) ; Horníková, Lenka (referee)
The hepatitis C virus (HCV) is a major etiological agent of chronic liver diseases. More than 170 million people worldwide are chronically infected, and more than 100 thousand of them develop hepatocellular carcinoma a year. HCV is an enveloped, positive-sense single-stranded RNA virus (+ssRNA virus) of the family Flaviviridae. Its genome is translated to produce a single polyprotein precursor that is further processed by cellular and viral proteases to form 10 viral proteins. Moreover, there is another protein encoded in an alternative reading frame. Two alternative translation mechanisms have been proposed for expression of this alternative reading frame protein (ARFP): a frameshift mechanism and translation initiating from internal start codons. Despite ten years of research its role in vivo is not yet explained. It appears that secondary structures in the core encoding region of HCV genome but not ARFP expression are required for robust viral translation and replication. The results of recent studies suggest that mutations distorting these structures may result not only in slowing down the viral cycle but also in a brand new and utterly unusual serological profile in patients as well as an increased level of expression of ARFP.
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