|
|
The use of numerical representations in processing of nucleotide sequences
Košíček, Adam ; Maděránková, Denisa (referee) ; Kubicová, Vladimíra (advisor)
Conversion of DNA sequences for appropriate representation is important task before initiation of analyzes and further processing. The main goal of this work was to get familiar with types of numerical and graphical representations and their application for DNA analyzes. In consideration of great volume of methods and procedures, only a few were chosen for this work. Some methods can not be classified only as numerical or graphical representations, because of option allowing them to be converted into both of these representations. These methods were classified as graphical representations. Phylogenetic trees were programmed for chosen methods to compare its precision. Outcome of this work is summing up the results.
|
|
|
Identification of coding regions using DNA spectrogram analysis
Spíchalová, Barbora ; Provazník, Ivo (referee) ; Kubicová, Vladimíra (advisor)
The Bachelor’s Thesis deals with coding identification of coding regions using DNA spectrogram analysis. The theoretical part describes numerical representations of genomic data and methods for editing DNA sequences. The types of methods used for DNA spektrogram construction and characteristic patterns detected by spectrogram are described. The most used method for data processing is discrete Fourier transformation that enables us to scan sequences for required data. There is also a theoretical part about creating a spectrogram and a list of detected samples. Knowledge of this is used to program specific methods in Matlab. We created a program for detection of coding parts in Spectrogram and defining their accurate positions in the sequence. Acquired results are discussed and compared with the NCBI database at the end of this work.
|
|
|
Comparison of methods for RGB spectrogram construction of DNA
Postránecká, Tereza ; Provazník, Ivo (referee) ; Kubicová, Vladimíra (advisor)
This thesis discusses about possibilities of construction colour DNA spectrograms and about patterns which can be detected there. Spectrograms as tools of spectral analysis give us a simultaneous view of the local frequency throughout the nucleotide sequence. They are suitable for gene identification or gene regions identification, determination of global character about whole chromosomes and also give us a chance for the discovery of yet unknown regions of potential significance. For purpose of this kind of DNA analysis is possible to use digital signal processing methods. We can apply them on only after conversion of DNA sequence to numerical representation. Selection of correct numerical representation affects how well will be reflected biological features in numerical record which we need for another use in digital signal analysis.
|
|
|
Fractal of DNA sequence data
Nedvěd, Jiří ; Čech, Petr (referee) ; Valla, Martin (advisor)
This project is looking for fractal structury in DNA sequence data, which be maped in square ACGT. First, this project is introduced in problematics of fractals and targeted on making of Sierpinski gasket. Second, the project is introduced in DNA and DNA sequence. Next is sketched now known fractal’s structures in DNA sequence data or fractal’s structure closed DNA sequence. Then will changed metod chaos game of Sierpinski gasket to square ACGT, in where will drawen map of DNA sequences. Next, these pictures will processed by Box Counting Method and Power Spectrum Method.
|
|
|
Graphical representation of DNA and protein sequences
Pražák, Ondřej ; Kolářová, Jana (referee) ; Maděránková, Denisa (advisor)
Modification of DNA sequences and their suitable representation is important part of analysis, comparison and another processing. Goal of this paper is finding of suitable methods for representation of genomic and proteomic sequences. Because there is great number of metods, this paper will introduce only some of them. All selected methods, are described in the first part of this paper and they were programed in Matlab. Selected methods are illustrated on coding sequences of the first exon of the b-globin gene of 11 different species. Results are compared withresults from the original papers. Some methods are capable of another processing like cluster analysis. Output of this paper is comparison of results, gained from different methods, and finding the most suitable one.
|
|
|
Hardware Acceleration of Algorithms for Approximate String Matching
Nosek, Ondřej ; Kořenek, Jan (referee) ; Martínek, Tomáš (advisor)
Methods for aproximate string matching of various sequences used in bioinformatics are crucial part of development in this branch. Tasks are of very large time complexity and therefore we want create a hardware platform for acceleration of these computations. Goal of this work is to design a generalized architecture based on FPGA technology, which can work with various types of sequences. Designed acceleration card will use especially dynamic algorithms like Needleman-Wunsch and Smith-Waterman.
|
|
|
Mitogenomic phylogeography and adaptive evolution of the bank vole Clethrionomys glareolus
Filipi, Karolína ; Kotlík, Petr (advisor) ; Munclinger, Pavel (referee)
This thesis is a part of the project aimed at sequencing the genome and transcriptome of the bank vole (Clethrionomys glareolus). The role of natural selection in the evolution of mitochondrial DNA (mtDNA) has been subject to much discussion; while some studies did not provide evidence that selection affected the phylogeography of the studied species, other considered adaptive evolution important. The bank vole is the key model we use to study the adaptation to climate change. As with other species, the phylogeography of the bank vole has been based on the variation of a small part of mtDNA. The goal of the thesis was to sequence the entire mitochondrial genome for representatives of all main mtDNA lineages of the bank vole using the Sanger and Illumina technologies, and to assess the role of selection and adaptation in the evolution and phylogeography of this species. The adaptive evolution in mtDNA probably was not the main driving force during the postlacial colonization of Europe. However, signatures of adaptive evolution have been found - an amino acid change with possible functional consequences in one gene and an excess of radical changes in physical- chemical properties of amino acids in populations at the latitudinal (northern and southern) extremes of the bank vole distribution. Key...
|
|
|
The use of numerical representations in processing of nucleotide sequences
Košíček, Adam ; Maděránková, Denisa (referee) ; Kubicová, Vladimíra (advisor)
Conversion of DNA sequences for appropriate representation is important task before initiation of analyzes and further processing. The main goal of this work was to get familiar with types of numerical and graphical representations and their application for DNA analyzes. In consideration of great volume of methods and procedures, only a few were chosen for this work. Some methods can not be classified only as numerical or graphical representations, because of option allowing them to be converted into both of these representations. These methods were classified as graphical representations. Phylogenetic trees were programmed for chosen methods to compare its precision. Outcome of this work is summing up the results.
|
|
|
Identification of coding regions using DNA spectrogram analysis
Spíchalová, Barbora ; Provazník, Ivo (referee) ; Kubicová, Vladimíra (advisor)
The Bachelor’s Thesis deals with coding identification of coding regions using DNA spectrogram analysis. The theoretical part describes numerical representations of genomic data and methods for editing DNA sequences. The types of methods used for DNA spektrogram construction and characteristic patterns detected by spectrogram are described. The most used method for data processing is discrete Fourier transformation that enables us to scan sequences for required data. There is also a theoretical part about creating a spectrogram and a list of detected samples. Knowledge of this is used to program specific methods in Matlab. We created a program for detection of coding parts in Spectrogram and defining their accurate positions in the sequence. Acquired results are discussed and compared with the NCBI database at the end of this work.
|
|
|
Gene Detection in DNA Sequences
Roubalík, Zbyněk ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
Gene detection in DNA sequences is one of the most difficult problems, which have been currently solved in bioinformatics. This thesis deals with gene detection in DNA sequences with methods using Hidden Markov Models. It contains a brief description of the fundamental principles of molecular biology, explains how genetic information is stored in DNA sequences, as well as the theoretical basis of the Hidden Markov Models. Further is described subsequent approach in the design of specific Hidden Markov Models for solving the problem of gene detection in DNA sequences. Is designed and implemented application, which uses previously designed Hidden Markov model for gene detection. This application is tested on the real data, results of these tests are discussed in the end of the thesis, as well as the possible extension and continuation of the project.
|
guest ::
