|
|
Automatic genotyping of bacteria by rep-PCR
Pelikánová, Veronika ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
This thesis deals with automatic bacteria genotyping by rep-PCR method. Its theoretical part presents various methods of DNA typing, basic information on electrophoresis and modern electrophoretic approaches, including their problems, misleading data distortion. In order to automate typing, there has been introduced a program for phylogenetic sample classification from rep-PCR, also applicable for data from chip capillary electrophoresis. The program consists of three main parts: digitization, bandmatching and clustering apparatus to bacterial type classification. The result of the algorithm is a phylogenetic tree, which indicates the cluster of sapmles according to bacterial type. The program has a graphical user interface for possible use in the Children's Hospital. Finally, the program is tested with data from the Children´s Hospital.
|
|
|
Genotyping of Klebsiella pneumoniae isolates
Nykrýnová, Markéta ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
This master thesis deals with typing of Klebsiella pneumoniae isolates. The first part of the thesis introduces molecular typing methods. Then bacterial genomes and Klebsiella pneumoniae are characterized. Following part describes data validation, assembly of genomes and proposed algorithm for finding genes with high variability. In last part obtained results are presented and validated on other genomes of Klebsiella pneumoniae.
|
|
|
RNA secondary structure prediction
Hadwigerová, Michaela ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Since the time RNA has been discovered by the nature scientist Miescher the structure and function of it has been forgotten for a long time. The prime role in science had always DNA. An increase of interest in RNA came with the discovery of the tRNA structure and its catalytic and enzymatic properties. These discoveries led to a great development wave of bioinformatics and structure and function analysis of RNA.
|
|
|
Homology search using digital signal processing methods
Kamar, Yana ; Jugas, Robin (referee) ; Maděránková, Denisa (advisor)
Thesis includes the theoretical introduction to molecular biology and genetics on the necessary level, including a description of the structure of DNA and the homologous gene. Described are fixed and physic-chemical kinds of nucleotide mapping, methods for processing digital signals. Numerical representations of genes that were programmed in MATLAB: unwrapped and accumulated phases, density vectors. Using the unwrapped phase and density vectors with windows of different lengths was performed CDS searching in the entire genome by calculation metric distances (euclidean and canberian) and correlation. Also, using the metric distances, a homologous gene was found in more or less similar bacterial genomes. The result is the approximate threshold of distance (euclidean and canberian) using to find homologous genes in genome.
|
|
|
MHC and KIR genotyping of macaques in HIV infection research
Matula, Jan ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
Modern research of viral diseases relies on genomic data processing. Not only is the sequence of a virus important, genomic sequence of specific receptors in affected organisms also plays an important role. In this paper, a novel package for processing of next generation sequencing data in infectious disease written using R/Bioconductor language is proposed. Functionality of the package, including implementation of advanced SSAHA algorithm for fast database searches, is demonstrated using genotyping of genes for MHC and KIR receptors of HIV positive macaques.
|
|
|
Pozitive and negative selection of mitochondrial genome
Svoboda, Matěj ; Kupková, Kristýna (referee) ; Maděránková, Denisa (advisor)
The bachelor thesis engages with problematics of positive and negative selection of mitochondrial genome. Thesis is divided into two parts. First part grapples with theory and explanation of fundamental definitions, in particular understates mitochondrial genome, nucleotide mutation, positive and negative selection and furthermore evolution models. Second part focuses on processing mitochondrial DNA practically and on establishing functions in programming environment R. The emphasis is foremost on gene sequencing alignment and exploring substitutions. Consequently, obtained outcomes are contrasted with PAML and KaKs Calculator programme outcomes.
|
|
|
Whole genome alignment using suffix trees
Klouba, Lukáš ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
The aim of this thesis is to create an algorithm that allows the alignment of the genome of two organisms by means of suffix structures and to implement it into the programming language environment R. The thesis deals with the description of the construction of the suffix structures and the methods of whole genome alignment. The result of the thesis is a functional algorithm for whole genome alignment by means of suffix structures implemented in the software environment R and its comparison with similar programs for the whole genome alignment.
|
|
|
Identification of LTR retrotransposons in human genome
Trott, Eduard ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
Cílem této práce je zpracování literární rešerše na téma vyhledávání LTR retrotranspozonů v lidském genomu. Práce popisuje možné problémy spojedné s danou tématikou a obsahuje implementaci nového vhodného algoritmu pro vyhledávání. Výsledky tohoto algoritmu, obsahující všechny nalezené LTRs byly statisticky porovnány s existujícími algoritmy pro vyhledávání nových retroelementů.
|
|
|
Prediction of the replication origin in prokaryotic genomes
Lebó, Marko ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
This bachelor’s thesis deals with the problem of origin of replication (oriC) detection in genomes of prokaryotic organisms. It describes the differences in the processes of initiation of replication in organism of the both procaryotic domains – Bacteria and Archea. It describes the possibilities of conversion of DNA sequences into their numeric representaions and evaluates their application for oriC detection. Also, it describes different approaches in oriC detection and describes te functioning of already present programmes for oriC detection. Finally, it suggests a new tool for oriC detection in bacterial genomes – FindOri and discusses results, achieved during the testing of this tool.
|
|
|
A tool for assessing the quality of multiple sequence alignments
Pelikánová, Veronika ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
This thesis is dealing with quality assessment of multiple sequence alignments. It contains literature review of public available tools of multiple sequence alignments. The main part of this thesis focuses on the program on quality assessment of multiple sequence alignments (created with the help of various tools, using different settings, etc.). The program has a graphical user interface created in Matlab and is enclosed together with a set of nucleotide and protein sequences compiled for program testing and aplication. Last but not least, the thesis contains the assessment of public available tools resulting from program outputs.
|
guest ::
RSS feed.