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Mobile application for psychodiagnostics of preschool children
Guryča, Ondřej ; Smíšek, Radovan (referee) ; Škutková, Helena (advisor)
This bachelor thesis deals with the possibility of preschool children psychodiagnostics using a smartphone application. It is focused on the principle of psychodiagnostics and its different approach to preschool children psychodiagnostics, there are also described tests used in nowaday psychodiagnostics. In the next part is presented the current implementation of the OS Android application with chosen tests. At the end is an explanation of the way of evaluating data and recommendations for using the app.
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Statistic evaluation of phylogeny of biological sequences
Vadják, Šimon ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
The master's thesis provides a comprehensive overview of resampling methods for testing the correctness topology of the phylogenetic trees which estimate the process of phylogeny on the bases of biological sequences similarity. We focused on the possibility of errors creation in this estimate and the possibility of their removal and detection. These methods were implemented in Matlab for Bootstrapping, jackknifing, OTU jackknifing and PTP test (Permutation tail probability). The work aims to test their applicability to various biological sequences and also to assess the impact of the choice of input analysis parameters on the results of these statistical tests.
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Automatic improvements of images from 1D gel electrophoresis
Kovář, Martin ; Vítek, Martin (referee) ; Škutková, Helena (advisor)
In this bachelor’s thesis are explained the basic principles of electrophoresis and its modalities with focusing on 1D gel electrophoresis. It describes analysis of an electrophoreogram and causes of its possible distortion, and states specifications of applications of the method in microbiology, genomics and proteomics. The practical part presents development, optimization and outputs of a programme for automatic electrophoreogram analysis, which was created in Matlab environment. The analysis contains lane and band detection and computation of samples’ molecular weight. The ending of the thesis is constituted by evaluating efficiency of detection and accuracy of weight computation.
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Pozitive and negative selection of mitochondrial genome
Svoboda, Matěj ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis deals with positive and negative selection detection in mitochondrial genome of invertebrates and vertebrates. The component of this paper is to interpret the theory of evolution and evolution models. The main objective of this bachelor thesis is to formulate the algorithm package for a positive and negative selection detection in a program environment, RStudio. Consequently, outcomes of algorithm are compared to values acquired by tool PAML.
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Fourier transformation for exon prediction
Rusina, Michal ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
In this bachelor thesis there are described the methods of the prediction of exon. The first part is aimed at the difference between the prokaryotic and eukaryotic organisms, the description of the DNA structure and the explanation of the terms exon and intron. The second section of the theoretic part includes four methods of the prediction of exons namely dynamic programming, neural networks, hidden Markov models and discrete Fourier transform. In the practical part there was created the program called Predikce_exonu that searches exons in nucleotide sequences and works on the principle of the Fourier transform. This algorithm together with 3 freely available programs was tested on 25 sequences and the success of their prediction was described by sensitivity and specificity.
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Predictive models in survival analysis
Hadwigerová, Michaela ; Vítek, Martin (referee) ; Škutková, Helena (advisor)
With ever-new methods of treatment in health care occures a requierement of comparing these new methods to the old methods in some effective way. This is particularly important for the further development of these methods. However, data that describe these facts could not be processed by normal procedures and therefore was in the field of statistics to create a new kind of methods. They are known as predictive models of survival analysis.
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Comparison of bacterial genomes obtained from second and third generation sequencing
Rumlerová, Tereza ; Škutková, Helena (referee) ; Nykrýnová, Markéta (advisor)
This bachelor thesis deals with sequencing technologies with a focus on the second and third generation of sequencers and platforms Illumina Miseq and Oxford Nanopore Technologies MinION. There is a description of an assembly of genomes with an example of the assembly of 6 genomes of a bacteria Klebsiella pneumoniae and a quality testing of these genomes. The final part contains a theoretical description and a practical implementation of selected methods for comparison of the assembled genomes, which come from two different sequencing platforms.
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Bacterial Pan-Genome Analysis
Lorková, Ema Marta ; Škutková, Helena (referee) ; Nykrýnová, Markéta (advisor)
This bachelor thesis deals with pan-genome analysis for bacterial populations. The first part specifies genome, pseudogenes, bacteria and its genome, and pan-genome including its components. Following part introduces four tools for pan-genome analysis. Testing of these tools against specific bacterial genome and their comparison is mentioned in practical part. Lastly, an algorithm is implemented for creating new pipeline, and a code and obtained results are described.
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Methods for phylogenetic supertree reconstruction
Kosíř, Kamil ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The Phylogenetic reconstruction has seen great development in the last 30 years. Computers have become more powerful and more generally accessible, and computer algorithms more sophisticated. It comes the effort of scientists to reconstruct the entire tree of life from a large amount of phylogenetic data. Just for this purpose are formed phylogenetic supertrees that allow the combination of all information gathered so far. The aim of this work is to find a method to construct supertree that will give correct results.
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Preprocessing of 1D gel electrophoresis image
Svozilová, Veronika ; Škutková, Helena (referee) ; Vítek, Martin (advisor)
The aim of this work is to propose an algorithm in MATLAB, allowing image processing and evaluation of one-dimensional gel electrophoresis. At first describes the detection of samples based on the horizontal segmentation of electrophoresis gel image, followed by detection of the minimum intensity values of the image, a vertical segmentation and determination of the sample boundaries in the image. The final phase involves testing of the method on publicly available images and evaluation of the results.
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