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ECG Cluster Analysis
Pospíšil, David ; Kozumplík, Jiří (referee) ; Klimek, Martin (advisor)
This diploma thesis deals with the use of some methods of cluster analysis on the ECG signal in order to sort QRS complexes according to their morphology to normal and abnormal. It is used agglomerative hierarchical clustering and non-hierarchical method K – Means for which an application in Mathworks MATLAB programming equipment was developed. The first part deals with the theory of the ECG signal and cluster analysis, and then the second is the design, implementation and evaluation of the results of the usage of developed software on the ECG signal for the automatic division of QRS complexes into clusters.
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The use of numerical representations in processing of nucleotide sequences
Košíček, Adam ; Maděránková, Denisa (referee) ; Kubicová, Vladimíra (advisor)
Conversion of DNA sequences for appropriate representation is important task before initiation of analyzes and further processing. The main goal of this work was to get familiar with types of numerical and graphical representations and their application for DNA analyzes. In consideration of great volume of methods and procedures, only a few were chosen for this work. Some methods can not be classified only as numerical or graphical representations, because of option allowing them to be converted into both of these representations. These methods were classified as graphical representations. Phylogenetic trees were programmed for chosen methods to compare its precision. Outcome of this work is summing up the results.
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Similarity/dissimilarity analysis of genomic data on the basis of graphical representation
Těthal, Jiří ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
The work deals with the identification of species of animal through the density of nucleotids of mitochondrial gene CO1. In the first part the theory summarized information about DNA barcoding and the mitochondria, cellular organel that with this method is closely related. The second part deals with virtually comparing different sequences using the density of nucleotides. For this it was created program, which uses two functions, the first of the specified nucleotide sequence calculates the density and one can compare the density by distance methods.
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Digital image analysis of mitotic chromosomes
Hávová, Mariana ; Babula, Petr (referee) ; Škutková, Helena (advisor)
Changes in chromosome number and structure may cause serious diseases. Cytogenetic tests leadin to set of karyotype are done for detecting these abnormalities. Chromosomes are visualised with proper methods and karyotype is made up most often. Manual karyotyping is time-consuming and expensive task. Because of this, researchers have been developing automated karyotyping systems. Karyotyping systems classify chromosomes into classes based on their characteristic features. Overlapping and bent chromosomes are limitations for automatic classification since they ocur at almost every mitosis. Accuracy and reliability of karyotyping systems still depend on the human intervention. Overcoming of these problems and development of fully automated system is the aim of modern approaches.
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Use of Knowledge Discovery for Data from PDF Files
Dvořáček, Libor ; Burgetová, Ivana (referee) ; Bartík, Vladimír (advisor)
This bachelor thesis deals with the extraction of tables from digitally created pdfs and the subsequent use of the obtained data for data analysis. Methods of dimension reduction and cluster analysis are used. The main content is an analysis of available tools for data extraction in the python language, a description and comparison of the used machine learning methods and implementation of an application that combines all these topics into one functional unit at: http://extraktor.herokuapp.com
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Cluster Analysis
Chrobák, Martin ; Ronzhina, Marina (referee) ; Kozumplík, Jiří (advisor)
This master’s thesis is engaged in usage of cluster analysis for ECG signal to separate normal QRS complexes from abnormal ones. For this, it is used two algorithms created in professional computing interface MATLAB. The outputs from this master’s thesis are dendrograms, which divide QRS complexes into abnormal and normal clusters, and Pearson correlation coefficients.
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Bootstrap methods in phylogenetics
Sedlář, Karel ; Vohánka,, Jaroslav (referee) ; Škutková, Helena (advisor)
In recent decades, phylogenetic reconstruction has noted great development. It was achieved by using newly acquired molecular characteristics and processing that it began to be taken as an objective science. Rapid development showed that it is necessary to evaluate the results because new techniques provided phylograms from unreliable data. For these purposes, statistical sampling methods have been applied to the phylogeny, of which bootstrapping began later to dominate. However, it also has limitations, which should be considered during interpreting the results it provided to us. This work demonstrates by combining the principles of bootstrapping and consensus trees we can obtain phylograms with better properties than those of conventional phylograms.
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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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Verification of fermentative process of grape juice
Procházková, Lenka ; Nováková, Olga (referee) ; Vránová, Dana (advisor)
This thesis deals with identification of yeasts isolated during spontaneous fermentation of grape juice. For analysis the Pinot Noir grape variety grown in the integrated vineyard was chosen. In the theoretical part of this thesis basic information about yeasts are described. Genera of yeasts that occurs during fermentation process and methods based on PCR are also described. In this thesis PCR-RFLP method was used for identification of yeasts. The amplification of the 5,8S-ITS rDNA sequence was performed by the polymerase chain reaction with use of the primers ITS1 and ITS4. The restriction analysis was performed by applying five restriction endonucleases: HaeIII, HinfI, Taq?, AluI, MseI. The amplicons were split into fragments which length and number are typical for the particular species. These fragments were identified by agarose gel electrophoresis and electrophoreograms were evaluated by BioNumerics software. Dendrograms representing genetic similarity of isolated wine yeasts were created by using UPGMA cluster analysis.
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Monitoring of wine yeasts population during fermentation of wine cider
Krätschmerová, Kateřina ; Vojtíšková, Marie (referee) ; Vránová, Dana (advisor)
This thesis deals with identification of wine yeasts isolated during fermentation process of wine cider and grapes of Sauvignon grape variety, grown in the integrated vineyard. The identification and taxonomic classification is faster and easier due to the progress of molecular methods. In this thesis PCR-RFLP method was used for identification of yeasts. Sequences of DNA specific for each species were analysed. These sequences were amplified by means of PCR method and by using ITS1 and ITS4 primers. In following step, they were put through the restrictiction analysis with five restriction endonucleases. Fragments of DNA were separated by horizontal electrophoresis. The electrophoreograms were evaluated by BioNumerics software and final dendrogram representing genetics similarity of isolated yeasts was created by using UPGMA claster analysis. The basic information about yeasts and their identification by molecular methods are described in the theoretical part of this thesis.
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