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Fourier transformation for exon prediction
Rusina, Michal ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
In this bachelor thesis there are described the methods of the prediction of exon. The first part is aimed at the difference between the prokaryotic and eukaryotic organisms, the description of the DNA structure and the explanation of the terms exon and intron. The second section of the theoretic part includes four methods of the prediction of exons namely dynamic programming, neural networks, hidden Markov models and discrete Fourier transform. In the practical part there was created the program called Predikce_exonu that searches exons in nucleotide sequences and works on the principle of the Fourier transform. This algorithm together with 3 freely available programs was tested on 25 sequences and the success of their prediction was described by sensitivity and specificity.
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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.
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Analysis of intron sequence variability
Kukačková, Hana ; Provazník, Ivo (referee) ; Kubicová, Vladimíra (advisor)
This bachelor thesis reviews genetic expression, the main characteristics of introns, their importance, and the methodology of their recognition. Practical part focuses on intron variability analysis and conservative sequences searching. In the beginning, there is a structure of nucleic acids with their chemical and physical characteristics reviewed, follow by gene expression description with all steps – transcription, posttranscriptional splicing and translation. Afterwards, there is an analysis of introns importance, introns evolution theories and similarities among different organisms mentioned, follow by some introns recognition methods. Practical part is focused on the initial and terminal regions of introns and conservative dinucleotide sequences verifying. The thesis studies intron – exon and exon – intron boundaries. The last part tries to suggest new potentially conservative sequences – patterns, search for them and check their conservativeness.
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Molecular phylogeography of the tench Tinca tinca (Linnaeus, 1758)
Lajbner, Zdeněk ; Kotlík, Petr (advisor) ; Flajšhans, Martin (referee) ; Macholán, Miloš (referee)
The tench Tinca tinca (Linnaeus, 1758) is a valued table fish native to Europe and Asia, but which is now widely distributed in many temperate freshwater regions of the world as the result of human-mediated translocations. Spatial genetic analysis applied to sequence data from four unlinked loci (introns of three nuclear genes and mitochondrial DNA) defined two groups of populations that were little structured geographically but were significantly differentiated from each other, and it identified locations of major genetic breaks, which were concordant across genes and were driven by distributions of two major phylogroups. This pattern most reasonably reflects isolation in two principal glacial refugia and subsequent range expansions, with the Eastern and Western phylogroups remaining largely allopatric throughout the tench range. However, this phylogeographic variation was also present in European cultured breeds and some populations at the western edge of the native range contained the Eastern phylogroup. Thus, natural processes have played an important role in structuring tench populations, but human-aided dispersal have also contributed significantly, with the admixed genetic composition of cultured breeds most likely contributing to the introgression. I have then designed novel PCR-RFLP assays...
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Fourier transformation for exon prediction
Rusina, Michal ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
In this bachelor thesis there are described the methods of the prediction of exon. The first part is aimed at the difference between the prokaryotic and eukaryotic organisms, the description of the DNA structure and the explanation of the terms exon and intron. The second section of the theoretic part includes four methods of the prediction of exons namely dynamic programming, neural networks, hidden Markov models and discrete Fourier transform. In the practical part there was created the program called Predikce_exonu that searches exons in nucleotide sequences and works on the principle of the Fourier transform. This algorithm together with 3 freely available programs was tested on 25 sequences and the success of their prediction was described by sensitivity and specificity.
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Analysis of intron sequence variability
Kukačková, Hana ; Provazník, Ivo (referee) ; Kubicová, Vladimíra (advisor)
This bachelor thesis reviews genetic expression, the main characteristics of introns, their importance, and the methodology of their recognition. Practical part focuses on intron variability analysis and conservative sequences searching. In the beginning, there is a structure of nucleic acids with their chemical and physical characteristics reviewed, follow by gene expression description with all steps – transcription, posttranscriptional splicing and translation. Afterwards, there is an analysis of introns importance, introns evolution theories and similarities among different organisms mentioned, follow by some introns recognition methods. Practical part is focused on the initial and terminal regions of introns and conservative dinucleotide sequences verifying. The thesis studies intron – exon and exon – intron boundaries. The last part tries to suggest new potentially conservative sequences – patterns, search for them and check their conservativeness.
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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.
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