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Gene order in eukaryotic genomes: an analysis using sequence-based gene expression data
Divina, Petr ; Forejt, Jiří (advisor) ; Pačes, Jan (referee) ; Mokrejš, Martin (referee)
ZÁVĚRY 61 6. ZÁVĚRY 6.1. Analýza genů exprimovaných v myším varleti a jejich uspořádání v genomu Pomocí expresního profilování metodou SAGE (sériová analýza genové exprese) byl vytvořen katalog genů exprimovaných ve varleti dospělých myší. Byly identifikovány poziční klastry genů na chromosomech obsahující geny s preferenční expresí ve varleti. Tyto klastry obsahovaly signifikantně vyšší počet genů než v náhodně vygenerovaných genomech. Geny specificky exprimované v somatických buňkách myšího varlete byly signifikantně obohacené na chromosomu X, což podporuje teorii o hromadění genů preferenčně exprimovaných v samčích tkáních na chromosomu X. Geny exprimované z chromosomu X byly ochuzené v transkriptomu celého myšího varlete, což je v souladu s představou o inaktivaci chromosomu X během prvního meiotického dělení. Byla vytvořena veřejně přístupná internetová databáze Mouse SAGE Site, která shromažďuje expresní data z myších tkání a buněčných liniích vytvořená pomocí metody SAGE. 6.2. Genový obsah chromosomu Z kura domácího Chromosom Z kura domácího byl signifikantně obohacený o geny preferenčně exprimované v samčím mozku. ZÁVĚRY 62 Geny s preferenční expresí v samičím mozku vykazovaly náznak ochuzení na chromosomu Z. Podobně, geny specificky exprimované ve vaječnících byly na chromosomu Z...
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NA2Dsearch: a fast and easy tool for secondary structure searches through databases of nucleic acids in parallel
Hlubuček, Petr ; Mokrejš, Martin (advisor) ; Novotný, Marian (referee)
The diploma thesis is dealing with searching in secondary structures of nucleic acids. The NA2Dsearch application was developed that allows to search databases of secondary structures for a structural motif. The application offers user-friendly graphical user interface where a query motif can be constructed in comfortable visual way using drag&drop, database and result structures can be browsed and visualized. The application contains original interactive nucleic acid structure visualization algorithm and novel search algorithm. The search algorithm can perform a motif search on structural data (unlike existing programs that can perform a motif search on sequence data). The motif search means that a query is created that describes the structure of motif of our interest with variabilities (e.g. the length of hairpin loop) that can be tolerated. Search results are ordered by the score computed according to the resemblance of hit and the query. The NA2Dsearch also supports searching in sequence data which are folded by external folding program. Searching capabilities are demonstrated on several search experiments involving HCV IRES and tRNA. Three searches for HCV IRES were performed: a search for HCV IRES structure in database of more than thousand of HCV genomic sequences, a folding analysis of HCV IRES...
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Hidden Markov models as a tool for protein secondary structure prediction
Kraus, Ondřej ; Novotný, Marian (advisor) ; Mokrejš, Martin (referee)
Hidden Markov models are ideal tool for sequence analysis therefore they are used also for protein secondary structure prediction. A number of tools for protein secondary structure prediction exist today a part of them utilizes also hidden Markov models. Hence I try to introduce them to a reader and explain him the way they work and their advantages and disadvantages in this assay. The majority of methods predict three secondary structures with accuracy between 60% and 80% nevertheless with regard to different testing methodologies the results should be treated solely as indicative. Key-words: protein structure prediction, hidden Markov model, secondary structure
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Analysis of selected secondary structures of nucleic acids
Skružný, Petr ; Mokrejš, Martin (advisor) ; Drda Morávková, Alena (referee)
This work introduces a database of experimentally verified structures of nucleic acids which were collected from published scientific literature. The database is annotated and the structures are analysed from the perspective of quality and it was found that the experimentally obtained data are not always sufficient - their supporting evidence is often limited and their quality is not convincing. This work also discusses some of the problems, that can be encountered when the structures are experimentally probed. Contents of the database were compared to the RFAM database and despite of its small range it contains 80 new structures. The complete database of 166 structures can be possibly used to optimise software used to predict derived structures of nucleic acids. Furthermore, the work presents several possible ways of improvement of the quality of contained structures.
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Study of genome and transcriptome variability employing data processing from massive parallel DNA sequencing.
Vojta, Petr ; Hajdúch, Marián (advisor) ; Budinská, Eva (referee) ; Mokrejš, Martin (referee)
Massive parallel sequencing (MPS) data analysis tasks are often computationally demanding and their execution time would take too long using standard computing machines. Thus there is a need for parallelization of this tasks and ability to execute them on a sufficiently powerful computing machines. In the first chapter we describe a newly created platform for resequencing analysis of MPS data - MOLDIMED and novel annotation tool, which is ready to deploy on HPC infrastructure. The second chapter describes MPS approaches in Diamond-Blackfan anaemia (DBA), which is predominantly underlined by mutations in genes encoding ribosomal proteins (RP); however, its etiology remains unexplained in approximately 25% of patients. We performed panel sequencing of all ribosomal genes in DBA patient without previously known molecular pathology. A novel heterozygous RPS7 mutation coding RPS7 p.V134F was found in one female patient and subsequently confirmed in two asymptomatic family members, in whom mild anemia were detected on further examination. Subsequently, we performed whole transcriptome analysis in all family members and patient with RPS7 mutation in comparison with healthy control group and with DBA patients with known mutation in RPS19. We observed dysregulation mainly in signal pathways of translation,...
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Gene order in eukaryotic genomes: an analysis using sequence-based gene expression data
Divina, Petr ; Forejt, Jiří (advisor) ; Pačes, Jan (referee) ; Mokrejš, Martin (referee)
ZÁVĚRY 61 6. ZÁVĚRY 6.1. Analýza genů exprimovaných v myším varleti a jejich uspořádání v genomu Pomocí expresního profilování metodou SAGE (sériová analýza genové exprese) byl vytvořen katalog genů exprimovaných ve varleti dospělých myší. Byly identifikovány poziční klastry genů na chromosomech obsahující geny s preferenční expresí ve varleti. Tyto klastry obsahovaly signifikantně vyšší počet genů než v náhodně vygenerovaných genomech. Geny specificky exprimované v somatických buňkách myšího varlete byly signifikantně obohacené na chromosomu X, což podporuje teorii o hromadění genů preferenčně exprimovaných v samčích tkáních na chromosomu X. Geny exprimované z chromosomu X byly ochuzené v transkriptomu celého myšího varlete, což je v souladu s představou o inaktivaci chromosomu X během prvního meiotického dělení. Byla vytvořena veřejně přístupná internetová databáze Mouse SAGE Site, která shromažďuje expresní data z myších tkání a buněčných liniích vytvořená pomocí metody SAGE. 6.2. Genový obsah chromosomu Z kura domácího Chromosom Z kura domácího byl signifikantně obohacený o geny preferenčně exprimované v samčím mozku. ZÁVĚRY 62 Geny s preferenční expresí v samičím mozku vykazovaly náznak ochuzení na chromosomu Z. Podobně, geny specificky exprimované ve vaječnících byly na chromosomu Z...
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Hidden Markov models as a tool for protein secondary structure prediction
Kraus, Ondřej ; Novotný, Marian (advisor) ; Mokrejš, Martin (referee)
Hidden Markov models are ideal tool for sequence analysis therefore they are used also for protein secondary structure prediction. A number of tools for protein secondary structure prediction exist today a part of them utilizes also hidden Markov models. Hence I try to introduce them to a reader and explain him the way they work and their advantages and disadvantages in this assay. The majority of methods predict three secondary structures with accuracy between 60% and 80% nevertheless with regard to different testing methodologies the results should be treated solely as indicative. Key-words: protein structure prediction, hidden Markov model, secondary structure
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Analysis of selected secondary structures of nucleic acids
Skružný, Petr ; Mokrejš, Martin (advisor) ; Drda Morávková, Alena (referee)
This work introduces a database of experimentally verified structures of nucleic acids which were collected from published scientific literature. The database is annotated and the structures are analysed from the perspective of quality and it was found that the experimentally obtained data are not always sufficient - their supporting evidence is often limited and their quality is not convincing. This work also discusses some of the problems, that can be encountered when the structures are experimentally probed. Contents of the database were compared to the RFAM database and despite of its small range it contains 80 new structures. The complete database of 166 structures can be possibly used to optimise software used to predict derived structures of nucleic acids. Furthermore, the work presents several possible ways of improvement of the quality of contained structures.
|
|
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NA2Dsearch: a fast and easy tool for secondary structure searches through databases of nucleic acids in parallel
Hlubuček, Petr ; Mokrejš, Martin (advisor) ; Novotný, Marian (referee)
The diploma thesis is dealing with searching in secondary structures of nucleic acids. The NA2Dsearch application was developed that allows to search databases of secondary structures for a structural motif. The application offers user-friendly graphical user interface where a query motif can be constructed in comfortable visual way using drag&drop, database and result structures can be browsed and visualized. The application contains original interactive nucleic acid structure visualization algorithm and novel search algorithm. The search algorithm can perform a motif search on structural data (unlike existing programs that can perform a motif search on sequence data). The motif search means that a query is created that describes the structure of motif of our interest with variabilities (e.g. the length of hairpin loop) that can be tolerated. Search results are ordered by the score computed according to the resemblance of hit and the query. The NA2Dsearch also supports searching in sequence data which are folded by external folding program. Searching capabilities are demonstrated on several search experiments involving HCV IRES and tRNA. Three searches for HCV IRES were performed: a search for HCV IRES structure in database of more than thousand of HCV genomic sequences, a folding analysis of HCV IRES...
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