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DNA Microarrays Data Analysis
Hebelka, Tomáš ; Jaša, Petr (referee) ; Burgetová, Ivana (advisor)
This work concerns with data analysis of DNA microarrays by using cluster analysis. It explains biological terms - gene expression and DNA microarray. Next, it contains mathematical and informatical description of clustering methods and describes a way to apply these methods to microarrays data. Next, the work contains implementation's detail of clustering methods k-means, DBSCAN and introduces an original clustering algorithm Strom++. Then, description of implementation and application manual follow. Finally, accomplished results are evaluated.
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Microarray Data Analysis
Vogel, Ivan ; Smrž, Pavel (referee) ; Šilhavá, Jana (advisor)
The aim of this bachelor thesis is to describe the DNA microarray technology. Several analytical algorithms are discussed. It describes closely the clustering methods, especially several hierarchical clustering modifications. It gives a summary of available commercial and uncommercial software for microarray analysis. The thesis describes own implementation design of hierarchical methods. At the end, results are compared with similar uncommercial software.
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Genom analysis of \kur{Pseudomonas syringae} pathovars and design of suitable oligonucleotides for design of DNA chip
BERAN, Pavel
Pseudomonas syringae van Hall 1902 (Ps) is important bacterial pathogen parasiting on wide spectrum of plants. Ps is sorted to pathovars according to host plant. The aim of this thesis was determining of genome size using restriction cleavage and PFGE on available Ps pathovars, sequencing of selected genes and oligonucleotide design for assembling DNA microarray. Genome sizes determined by restriction cleavage and separation with PFGE were different from database data by about 500 {--} 2000 kbp. Therefore the method is less usefull for accurate determining of genome size. Genes for 16S and 23S rRNA, 16S-23S ITS and gyrB were sequenced mutual variability of Ps pathovars was evaluated and compared to similar works. DNA sequencing was also basis for oligonucleotide DNA chip design.
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Microarray Data Analysis
Vogel, Ivan ; Smrž, Pavel (referee) ; Šilhavá, Jana (advisor)
The aim of this bachelor thesis is to describe the DNA microarray technology. Several analytical algorithms are discussed. It describes closely the clustering methods, especially several hierarchical clustering modifications. It gives a summary of available commercial and uncommercial software for microarray analysis. The thesis describes own implementation design of hierarchical methods. At the end, results are compared with similar uncommercial software.
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DNA Microarrays Data Analysis
Hebelka, Tomáš ; Jaša, Petr (referee) ; Burgetová, Ivana (advisor)
This work concerns with data analysis of DNA microarrays by using cluster analysis. It explains biological terms - gene expression and DNA microarray. Next, it contains mathematical and informatical description of clustering methods and describes a way to apply these methods to microarrays data. Next, the work contains implementation's detail of clustering methods k-means, DBSCAN and introduces an original clustering algorithm Strom++. Then, description of implementation and application manual follow. Finally, accomplished results are evaluated.
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