|
|
Visualization of DNA Secondary Structures in R/Bioconductor
Jaroš, Marta ; Bendl, Jaroslav (referee) ; Martínek, Tomáš (advisor)
This bachelors thesis deals with the visualization techniques of the secondary structures of DNA. It summarizes and discusses some of the current methods of visualization. It explains the problem and its importance from the standpoint of molecular biology. The main aim of the work is the design of a generic algorithm for visualization of secondary structures of DNA, specifically palindromes and triplexes, and its implementation into the environment R/Bioconductor. It focuses in particular on the area of 2D graphical imaging of these secondary structures of DNA. The result of the work is 2D visualization support for R/Bioconductors software packages which provide searching of the characteristic sequence of palindromes and triplexes in DNA sequences.
|
|
|
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.
|
|
| |
|
|
Optimization of Algorithms for Triplex Detection
Hon, Jiří ; Bendl, Jaroslav (referee) ; Martínek, Tomáš (advisor)
Triplex-forming DNA sequences have been implicated as important players in several key processes, such as transcriptional regulation, DNA recombination and mutagenesis, which emphasize their importance for biology, biotechnology and medicine. This bachelor thesis optimizes recently publicated dynamic programming algorithm for identification of triplex-forming sequences on three levels of design: user interface, memory usage and computation time. On the level of user interface, the algorithm was extended with existing visualization functions and rewritten into R/Bioconductor package. Memory usage optimization and processor cache analysis in combination with computation time reduction based on current computation state analysis lead to more than three times acceleration.
|
|
|
Function of Magnesium Ions in the Formation of Biologically-Active Nucleic Acids Structures
Espinoza Herrera, Shirly Josefina ; Štěpánek, Josef (advisor) ; Mašek, Vlastimil (referee) ; Setnička, Vladimír (referee)
ESPINOZA HERRERA S.J. - DOCTORAL THESIS - FUNCTION OF MAGNESIUM IONS IN THE FORMATION OF BIOLOGICALLY-ACTIVE NUCLEIC ACIDS STRUCTURES ____________________________________________________________________ ABSTRACT Interaction of magnesium ions, the divalent ions with the highest concentration inside living cells, with the key biomolecules of nucleic acids was studied with aim to find out structural details of the interaction mechanism and effect of the magnesium ions presence on the nucleic-acid structure and structural transitions. Raman spectroscopy was chosen as the main experimental method, some complementary measurements of UV absorption spectra were also performed. Basic analyses of the spectral series obtained as a function of temperature and/or for various concentrations of Mg2+ ions were done by means of factor analysis. Where possible the factor analysis outputs were used for fits of appropriate thermodynamic equations. For the studies, various nucleic-acid molecular models were employed, in particular complementary RNA homopolynucleotides polyA and polyU, DNA homopolynucleotides polydA and polydT and RNA 14-mer oligonucleotide representing the apical hairpin of the TAR segment of HIV-1 genomic RNA. We have confirmed via Raman spectroscopy that magnesium ions added to a solution of polyA-polyU...
|
|
| |
|
|
Function of Magnesium Ions in the Formation of Biologically-Active Nucleic Acids Structures
Espinoza Herrera, Shirly Josefina ; Štěpánek, Josef (advisor) ; Mašek, Vlastimil (referee) ; Setnička, Vladimír (referee)
ESPINOZA HERRERA S.J. - DOCTORAL THESIS - FUNCTION OF MAGNESIUM IONS IN THE FORMATION OF BIOLOGICALLY-ACTIVE NUCLEIC ACIDS STRUCTURES ____________________________________________________________________ ABSTRACT Interaction of magnesium ions, the divalent ions with the highest concentration inside living cells, with the key biomolecules of nucleic acids was studied with aim to find out structural details of the interaction mechanism and effect of the magnesium ions presence on the nucleic-acid structure and structural transitions. Raman spectroscopy was chosen as the main experimental method, some complementary measurements of UV absorption spectra were also performed. Basic analyses of the spectral series obtained as a function of temperature and/or for various concentrations of Mg2+ ions were done by means of factor analysis. Where possible the factor analysis outputs were used for fits of appropriate thermodynamic equations. For the studies, various nucleic-acid molecular models were employed, in particular complementary RNA homopolynucleotides polyA and polyU, DNA homopolynucleotides polydA and polydT and RNA 14-mer oligonucleotide representing the apical hairpin of the TAR segment of HIV-1 genomic RNA. We have confirmed via Raman spectroscopy that magnesium ions added to a solution of polyA-polyU...
|
|
|
Visualization of DNA Secondary Structures in R/Bioconductor
Jaroš, Marta ; Bendl, Jaroslav (referee) ; Martínek, Tomáš (advisor)
This bachelors thesis deals with the visualization techniques of the secondary structures of DNA. It summarizes and discusses some of the current methods of visualization. It explains the problem and its importance from the standpoint of molecular biology. The main aim of the work is the design of a generic algorithm for visualization of secondary structures of DNA, specifically palindromes and triplexes, and its implementation into the environment R/Bioconductor. It focuses in particular on the area of 2D graphical imaging of these secondary structures of DNA. The result of the work is 2D visualization support for R/Bioconductors software packages which provide searching of the characteristic sequence of palindromes and triplexes in DNA sequences.
|
|
|
Optimization of Algorithms for Triplex Detection
Hon, Jiří ; Bendl, Jaroslav (referee) ; Martínek, Tomáš (advisor)
Triplex-forming DNA sequences have been implicated as important players in several key processes, such as transcriptional regulation, DNA recombination and mutagenesis, which emphasize their importance for biology, biotechnology and medicine. This bachelor thesis optimizes recently publicated dynamic programming algorithm for identification of triplex-forming sequences on three levels of design: user interface, memory usage and computation time. On the level of user interface, the algorithm was extended with existing visualization functions and rewritten into R/Bioconductor package. Memory usage optimization and processor cache analysis in combination with computation time reduction based on current computation state analysis lead to more than three times acceleration.
|
|
|
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.
|
guest ::
