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Management tool for sequence types database of pathogenic bacteria
Františová, Zuzana ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
The objective of this bachelor thesis is to design and create a management tool for sequence types database of pathogenic bacteria. The basis of this thesis is the designing a transfer key for the new molecular technique for typing of bacteria, which was created in cooperation with Centre of Molecular Biology and Gene Therapy, Department of Internal Medicine – Haematooncology, University Hospital Brno. The new method is based on translation sequence type to appropriate melt type. In the first two chapters, the advantages and disadvantages of the most used methods in molecular biology and the most favorite typing methods are discussed. Another three chapters introduce designing of the transfer key, its implementation in the MATLAB environment and the final management tool consisted of two programmes. The first program includes transfer key computation and the second program allows particular melt type and appropriate sequence types retrieval, which is an easy way to compare sequential and PCR data.
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Bacterial species delineation based on parameters derived from numerical representations of genome
Oweis, Kamil ; Jugas, Robin (referee) ; Maděránková, Denisa (advisor)
Modern methods of processing genomic data yield good results, however they are often redeemed by time consummation. This is mainly the reason why this thesis deals with numerical methods of bacterial genome processing which could be a suitable alternative for current methods, both in terms of quality and computational demands. This thesis presents the current methods used for processing of genomes in silico and proposes suitable numerical presentations for the whole genome analysis. Some of these methods are programmed and used for processing further in this diploma thesis. In it, various mathematical and statistical methods are being tested, ones that could lead to successful species delineation of bacteria by numerical presentations of their genomes.
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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.
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Fuzzy classification of DNA sequences
Těthal, Jiří ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The work deals with the fuzzy classification of DNA sequences. In the first part the theory summarized information about Fuzzy logic and methods of its use in the classification of biological sequence data. The second part is practically deal with the classification algorithm for assessing the similarity of sequences. Specifically, the dividing of coding and non-coding parts of the sequence and the use of fuzzy classification in DNA barcoding.
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Measuring of conformational properties of nucleic acids
Hrazdilová, Ivana ; Renčiuk,, Daniel (referee) ; Maděránková, Denisa (advisor)
This thesis gives a brief characteristic of the most important conformations of nucleic acids. It describes alternative conformations that are different from canonical B-DNA helix, such as A-DNA, Z-DNA, triplex structures, or guanine and cytozin quadruplex structures. In the next part it presents most common methods used for determing secondary structure of nucleic acids, which are nuclear magnetic resonance (NMR), measurement of circular dichroism (CD), X-ray diffraction, computational methods, measurements of ultraviolet absorbance and its utilization for analysis of thermal melting curves. In MATLAB was created algorithm with graphical user interface, which analyze melting curves and graphically computes thermodynamic parameters, which are melting temperature and transition enthalpy, which defines stability of examined sample.
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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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