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Digital signal processing of mitochondrial genomes
Sonnenschein, Jiří ; Vítek, Martin (referee) ; Škutková, Helena (advisor)
The aim of this thesis is to test new less hardware demanding method of mitochondrial genom classification, for which numerical representation of biological sequences is used. Introductory part is focused on description of nucleic acids and mitochondrion. In following part of thesis, types of numerical representation of biological sequences without losing the original biological information are described. There are introduced possibilities of phase and frequency-domain analysis and principles of cluster analysis and dendrogram construction methods. Practical part of this work deals with analysis of mitochondrial genome for which cumulated and unwrapped phases are calculated. Mitochondrial sequences are compared by cluster analysis and dendrogram is constructed.
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Biological sequence classification utilizing lossless data compression algorithms
Kruml, Ondřej ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
Tato diplomová práce se zabývá možností využití bezeztrátových kompresních algoritmů ke klasifikaci biologických sekvencí. Nejdříve je představena literární rešerše o bezeztrátových kompresních algoritmech, která byla využita k výběru slovníkového algoritmu vytvořeného A. Lempelem a J. Zivem v roce 1976 (LZ77). Tento algoritmus je běžně používán k datové kompresi a v předkládané práci byl modifikován tak, aby umožnil klasifikaci biologických sekvencí. K algoritmu byly navrženy další modifikace, které rozvíjí jeho klasifikační možnosti. V průběhu práce byla sestavena sada datasetů biologických sekvencí, která umožnila podrobné testování algoritmu. Algoritmus byl porovnán s klasickými zarovnávacími metodami: Jukes-Cantor, Tamura a Kimura. Bylo ukázáno, že algoritmus dosahuje srovnatelných výsledků v oblasti klasifikace biologických sekvencí a dokonce je u 20% datasetů překonává. Lepší výsledky dosahuje zejména u sekvencí, jež jsou si vzájemně vzdálené.
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Methods for fast sequence comparison and identification in metagenomic data
Kupková, Kristýna ; Škutková, Helena (referee) ; Sedlář, Karel (advisor)
Předmětem této práce je vytvoření metody sloužící k identifikaci organismů z metagenomických dat. Doposud k tomuto účelu spolehlivě dostačovaly metody založené na zarovnání sekvencí s referenční databází. Množství dat ovšem s rozvojem sekvenačních technik rapidně roste a tyto metody se tak stávají díky své výpočetní náročnosti nevhodnými. V této diplomové práci je popsán postup nové techniky, která umožňuje klasifikaci metagenomických dat bez nutnosti zarovnání. Metoda spočívá v převedení sekvenovaných úseků na genomické signály ve formě fázových reprezentací, ze kterých jsou následně extrahovány vektory příznaků. Těmito příznaky jsou tři Hjorthovy deskriptory. Ty jsou dále vystaveny metodě maximalizace věrohodnosti směsi Gaussovských rozložení, která umožňuje spolehlivé roztřídění fragmentů podle jejich příslušnosti k organismu.
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Methods to detect selection in DNA sequences
Procházka, Ondřej ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The topic of semestral thesis is methods to detect selection in DNA sequences. In the begining of the thesis we will describe molecular evolution. It will be written what made the evolution and how the evolution is shown. Moreover there are gen mutations and mechanisms of diffuse and fixation. It will be defined what pozitive, negative and neutral selection is. The thesis is focused on evolution distance of synonymous and nonsynonymous substitution. There will be described three methods – Nei-Gojobori, Li-Wu-Luo and Comeron. All these methods will be described with mathematic formulas. There will be statistic test to decide what kind of selection ti is – there will be used z-test. In the practical part, there will be information about developed software what counts selection pressure from sequences from databazes in format GenBank and it shows parts where selection is. The software will be used for two data sets with two different genetic codes. The result will be discussed. We will discuss results of all three methods of selection pressure and influence of input parametrs.
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Numerical methods for classification of metagenomic data
Vaněčková, Tereza ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
This thesis deals with metagenomics and numerical methods for classification of metagenomic data. Review of alignment-free methods based on nucleotide word frequency is provided as they appear to be effective for processing of metagenomic sequence reads produced by next-generation sequencing technologies. To evaluate these methods, selected features based on k-mer analysis were tested on simulated dataset of metagenomic sequence reads. Then the data in original data space were enrolled for hierarchical clustering and PCA processed data were clustered by K-means algorithm. Analysis was performed for different lengths of nucleotide words and evaluated in terms of classification accuracy.
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Use of molecular-genetic methods for research of colorectal carcinoma
Janáková, Tereza ; Škutková, Helena (referee) ; Provazník, Ivo (advisor)
The aim of this bachelor work is to carry out statistical analysis of mutations in KRAS, BRAF and PIK3CA genes. Introductory part is focused on colorectal carcinoma in general. In following part of the work, we discuss genetics of tumors, description of KRAS, BRAF and PIK3CA genes, molecular-genetic analytical methods, widely used in genetics, especially PCR. Further detection of mutations is described. In the next part of the work, we propose a method for detection of mutations in KRAS, BRAF and PIK3CA genes, which consist in using PCR and commercial kits. The following chapter "Results of Analysis of mutations" contains detailed grafical presentation of mutations. Frequencies of mutations were compared with published data and with data from laboratories in Pilsen and Prague. In the end of the bachalor work, there is summary of results and their possible benefit.
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Distance methods for reconstruction of phylogenetic trees
Šudák, Vítězslav ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
Thesis „Distance methods for reconstruction phylogenetic trees“ summarizes notes about methods for calculating evolutionary distances from aligned nucleotide, eminoacid or codon sequences. Then using these distances in methods for reconstructing phylogenetic trees from matrixes made of these distances. Aim is to create these method as a functional scripts in MATLAB software and appliance these method on real sequences downloaded from public databanks on internet in FASTA format, and to create a thesis about hese methods and describe them and my results.
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Evaluation of Organisms Relationship by Genomic Signal Processing
Škutková, Helena ; Tkacz, Ewaryst (referee) ; Schwarz,, Daniel (referee) ; Provazník, Ivo (advisor)
This dissertation deals with alternative techniques for analysis of genetic information of organisms. The theoretical part presents two different approaches for evaluation of relationship between organisms based on mutual similarity of genetic information contained in their DNA sequences. The first approach is currently standardized phylogenetics analysis of character based records of DNA sequences. Although this approach is computationally expensive due to the need of multiple sequence alignment, it allows evaluation of global and local similarity of DNA sequences. The second approach is represented by techniques for classification of DNA sequences in a form of numerical vectors representing characteristic features of their genetic information. These methods known as „alignment free“ allow fast evaluation of global similarity but cannot evaluate local changes. The new method presented in this dissertation combines the advantages of both approaches. It utilizes numerical representation similar to 1D digital signal, i.e. representation that contains specific trend along x-axis. The experimental part of dissertation deals with design of a set of appropriate tools for genomic signal processing to allow evaluation mutual similarity of taxonomically specific trends. On the basis of the mutual similarity of genomic signals, the classification in the form of dendrogram is applied. It corresponds to phylogenetic trees used in standard phylogenetics.
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Protein calculator
Sedlo, Petr ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
This work is focussed on studying and analysis of protein qualities while using experimental methods which are next confronted with numerical analysis, which have been introduced by the expansion in computer engineering. Within that task I built up a program for calculation of isoelectric point and molecular mass of an entered chain of amino acids. The program will draw a graph of pH dependance of molecular charge in the wide range of pH values in accordance with the given criteria. We can gain results very quickly and easily in this way, however, these results are just a rough estimate. We´re assumed to be aware of this fact because incorrect use of that program where exact analysis is required would cause errors.
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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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