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Character-based methods for DNA barcoding
Kalianková, Kateřina ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
This work deals with character-based DNA barcoding. DNA barcoding and character-based DNA barcoding methods are described in the introduction. Another part contains information of method CAOS (Characteristic Attributes Organization), method BLOG (Barcoding with LOGic) and method BLAST. Programs are described in the practical part. The end contains results.
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Synonymous codon usage bias in mitochondrial genomes
Urbanová, Hedvika ; Cicková, Pavlína (referee) ; Maděránková, Denisa (advisor)
This Bachelors thesis deals with synonymous codon usage bias in mitochondrial genomes. This thesis covers basic terms of bioinformatics and genetics. Codon usage bias is introduced together with parameters that characterize it. Practical part of the thesis is dealing with programs that are designed to calculate parameters of codon usage bias. Programs that are described in this thesis are relative synonymous codon usage, relative adaptation index, codon adaptation index, homozygosity of codons, and effective number of codons. Synonymous codon usage bias in mitochondrial genome of Homo sapiens is analysed.
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Fourier transformation and spectrogram analysis of DNA sequences
Krejčí, Michal ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Various methods of DNA sequences modifications for frequency analysis and basic characteristics of DNA are described in the theoretical part of this thesis. Tricolor spectrograms, created by short time Fourier transform help us to recognize some characteristic patterns in DNA sequences. Practical part of this work deals with developed programme which generates spectrograms and analyse them. Last part deals with the analysis of selected sequences of C. elegans genome. Some patterns are related to data of public databases such as NCBI. Various patterns are explained from the biological nature, which relates to chromosome structure and protein coding regions. Another well recognised patterns, tandem repetitions composed of satellites, microsatellites and minisatelites are described by spectrograms as well.
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Methods for multialignment of nucleotide sequences
Trněný, Ondřej ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
To be able to understand characteristics and purpose of biological sequences correctly, it is crucial to have a possibility to sort and compare them. Because of this need and to extend existing knowledge pool, numerous methods were proposed. Especially in field of multiple sequences alignment. Methods for multiple sequences alignment may provide various valuable information about sequences which failed to show enough similarity in pairwise alignment. According to this, several algorithms were implemented in various computer applications which provide a way to analyse huge sets of data. One of those, the progressive alignment algorithm, is implemented as a part of this thesis
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Effect of nucleotide density vector's reduction on molecular identification of organisms
Kosková, Markéta ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
This work deals with the effect of nucleotide density vector's reduction on molecular identification of organisms. At the beginning of the theoretical part, the work explains the concept of species, its development and its mutations. The next section provides basics of taxonomy, particularly the molecular taxonomy and DNA barcoding, with a description of mitochondrial DNA and its usability in the identification of species. The end of the theoretical part provides information about the nucleotide density vectors which the practical part is focused on. Analysis of auxiliary values on nucleotide density vectors was accomplished in Matlab by evaluating 188 real DNA barcode sequences. The identification analysis of organism was performed with the best auxiliary value for 4 datasets of the reference barcode sequences and 5 datasets of analyzed sequences of same organisms. Afterwards, the evaluation of the analysis was done by using separate nucleotide density vectors of individual nucleotides and their amounts.
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User interface for data extraction from GenBank data format
Jurečková, Kateřina ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis contains a literature review on the topic of the GenBank database, its most used flat file format gbk and its comparison with other formats of sequential data. Furthermore this thesis describes the structure of mitochondrial DNA of animals and plants and plastid DNA of plants. In the practical part of this thesis is evaluation of successful automatic data extraction from GenBank flat file format from whole mitochondrial sequences by genbankread function in Matlab. And it describes also a new application for GenBank data extraction. In the end this application is used in analyses of mitochondrial genomes.
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Numerical representations of protein sequences for classification
Bartoň, Vojtěch ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
Todays we have the opportunity to analyze huge sets of genomics and proteomics data. In my bachaleor thesis I introduce a few numerical alternatives to represent proteins. The usage of numerical representations opened the way to analyze proteomics data as digital signals, which bring us quantity of new possibilities how to process the protein. In my thesis I compare a few numerical representation with standard taxonomy and with symbolic representation too.
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Nucleotide density for finding CpG islands
Sikorová, Eva ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis deals with searching for CpG islands in the DNA sequences using the nucleotide density vectors. The first part includes view of the DNA structure, the genetic information expression, more detailed analysis of CpG islands and primarily their detection methods. In the practical part the algorithm for graphical representation of nucleotides on the basis of their densities and detections of CpG islands of artificially created and real DNA sequences was realized in the MATLAB program. The thesis includes the analysis of twenty sequences with the expected content of CpGIs and the comparison of results between the created program and two search engines.
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Mitochondrial DNA for molecular taxonomy
Kalianková, Kateřina ; Babula, Petr (referee) ; Maděránková, Denisa (advisor)
This work deals with mitochondrial DNA and molecular taxonomy. Structure and composition of animal cell, deoxyribonucleic acids and mitochondrial ribonucleic acids are described in the introduction. Another part contains information of DNA barcoding and numerical representation of genomic sequences. Programs are described in the practical part.
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Gene order conservation in bacterial genomes
Martinková, Tereza ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
Theoretical part of the thesis deals with basic concepts such as bacterial genome, comparative genomics and mainly synteny blocks. Here is explained what synteny is and what is its importance. In the theoretical part, the GenBank format is also mentioned, its content and usage. The practical part is focused on searching similarities in DNA sequences of reference bacteria with selected bacteria, their sorting by means of greedy algorithm and visualization of similarities using phylogenetic tree.
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