|
|
Web Application for Bioinformatics Education - Genetic Code
Kilián, Martin ; Martínek, Tomáš (referee) ; Burgetová, Ivana (advisor)
This thesis briefly describes basic informations in moleculary biology. Thesis deals with a transfer of information from DNA into RNA through uprotein, are also briefly described the methods and algorithms dealing with the detection of genome. The larger part deals with the recognition cue coded signals and determination of sequences and their subsequent transcription and translation, which demonstration program was needed to create. The final result is s web application as the education system.
|
|
|
Analysis of Genomic Data with the Assistance of Algorithm BLAST
Křížová, Martina ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This Bachelor Thesis describes analysis of genomic data with assistance of algorithm BLAST. In theoretic part, it describes genomes, their importance and structure. In this thesis, you can find a description of algorithm BLAST, Smith-Waterman and Needleman-Wunsch and with algorithm BLAST connected Karlin-Altschul statistics. This thesis is discussing types of databases such as spatial, deductive and relational which store genomic data. Second part is concerned with design and implementation of application which use mentioned algorithm and database Oracle 10g R2. Testing and confrontation output of algorithm is also a part of this work.
|
|
|
Microarray Data Interpretation
Ludwig, Petr ; Šilhavá, Jana (referee) ; Smrž, Pavel (advisor)
This Bachelor thesis explains the basics of biochip or microarray data interpretation, starting with short introduction to genetics, especially genetic information significance evaluating. The focus was set mainly on the set of scripts transforming and analyzing the sample data. The data used in this thesis are a result of biochip analysis of the Colon Tumor tissues. The secondary result represents disclosing the main marker for this particular type of cancer, the primary result is evaluation of marker significance in the context of signaling pathways. The resulting pathways are sorted by relevance.
|
|
|
Application for Alignment of DNA Parts
Kašpárek, Tomáš ; Žák, Jakub (referee) ; Rozman, Jaroslav (advisor)
This thesis deals with DNA sequences alignment methods with focus on execution speed of given task and its optimality. The outcome of this thesis results in multiple programs, which presents DNA alignment algorithms and their versions programmed with OpenCL libraries, which are optimized on calculation rate. Text of this thesis apprises reader with DNA alignment problematic and its importance in biology. Further, algorithms for DNA alignment and options of their speed-up using libraries like CUDA or OpenCL are presented.
|
|
|
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.
|
|
|
Attributes Calculating for Prediction of Effects of Mutation on Protein Function
Matějíček, Jiří ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This bachelor thesis deals with the bioinformatics techniques for the acquisition of attributes useful for prediction of mutation effects on the protein function. The work primarily aims to develop a user-friendly application for calculation of attributes of mutations from the protein sequence and structure. The developed application serves for integration of specialized tools such as FoldX. The standardized interface enables to implement additional computational tools and collect a diverse set of attributes from different sources. These attribute sets can then serve as an input for different prediction methods and help to improve predictions of mutation effects.
|
|
|
Bioinformatics of human genome
Kupková, Karolína ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Bachelor thesis deals with DNA segments containing only adenine and guanine. The theoretical part describes the structure and composition of deoxyribonucleic acid, chromosomes and genes. There are basic informations about chimpanzees and the human genome and conformations of the chains containing adenine with guanine. The practical part consists of a program that searches for the required sections in sequence, it displays and saves it. The thesis includes analysis of genes which are common for humans and chimpanzees, which were analyzed to determine randomness, functionality a preserving of these sections.
|
|
|
Diagnostics of genom conditioned diseases with the use of micro- and nanoparticles
Mondeková, Věra ; Prášek, Jan (referee) ; Provazník, Ivo (advisor)
The bachelor´s thesis discusses possibilities of viral genome´s detection through use of biosensors, more specifically through use of magnetic particles. The introductory part consists of brief characteristic of viruses, mentioned as originator of genom conditioned diseases, followed by chapters related to selected methods of nucleic acid´s extraction and analysis. The main part is dedicated to magnetic particles. The practical part of thesis deals with possibility of use of biosensors in specific viral pathogen´s detection, selection of biocompatible molecules suitable for magnetic particle modification and description of specific DNA sequence isolation procedure through use of magnetic particles.
|
|
|
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 ::
