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Predicting the Effect of Amino Acid Substitutions on Protein Function Using MAPP Method
Pelikán, Ondřej ; Vogel, Ivan (referee) ; Bendl, Jaroslav (advisor)
This thesis discusses the issue of predicting the effect of amino acid substitutions on protein function using MAPP method. This method requires the multiple sequence alignment and phylogenetic tree constructed by third-party tools. Main goal of this thesis is to find the combination of suitable tools and their parameters to generate the inputs of MAPP method on the basis of analysis on one massively mutated protein. Then, the MAPP method is tested with chosen combination of parameters and tools on two large independent datasets and consequently is compared with the other tools focused on prediction of the effect of mutations. Apart from this the web interface for the MAPP method was created. This interface simplifies the use of the method since the user need not to install any tools or set any parameters.
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Statistic evaluation of phylogeny of biological sequences
Zembol, Filip ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
The topic of my diploma thesis is the statistical evaluation of biological sequences with the help of phylogenic trees. In the theoretical part we will create a literary recherche of estimation methodology concerning the course of phylogeny on the basis of the similarity of biological sequences (DNA and proteins) and we will focus on the inaccuracies of the estimation, their causes and the possibilities of their elimination. Afterwards, we will compare the methods for the statistical evaluation of the correctness of the course of phylogeny. In the practical part of the thesis we will suggest algorithms that will be used for testing the correctness of the phylogenic trees on the basis of bootstrapping, jackknifing, OTU jackknifing and PTP test which are able to the capture phylogenic tree with the method neighbor joining from the biological sequences in FASTA code. It is also possible to change the distance model and the substitution matrix. To be able to use these algorithms for the statistical support of phylogenic trees we have to verify their right function. This verification will be evaluated on the theoretical sequences of the amino acids. For the verification of the correct function of the algorithms, we will carry out single statistical tests on real 10 sequences of mammalian ubiquitin. These results will be analysed and appropriately discussed.
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Identification of RNA elements in fungi
PÍCHALOVÁ, Barbora
Nowadays, the focus of fungus, mycovirus and environmental interactions has expanded. The kingdom of Fungi includes ecologically and economically important species of fungi that are pathogenic or symbiotic or can occur in the soil as mycorrhizal and endophytic fungi. Despite their ecological significance, biomedical and industrial importance, phylogenomic studies of Fungi and their viruses are lacking. To understand the basic interactions between mycoviruses and their fungal hosts, the study of the biological properties, distribution and transmission is required. This study aims to identify different species of fungi and determine the interaction between fungus and virus. Samples collected in the Czech Republic during 2020 and 2021 were used for diversity research and molecular genetic methods were chosen for their detection and identification. DNA was isolated using CTAB-PVP, the DNA segment was amplified and phylogenetically analyzed using the sequences of internal transcribed spacers (ITS), the translation elongation factor (TEF) 1-alpha gene and the beta-tubulin gene. Based on the sequences, a phylogenetic tree was created for the samples according to the genetic similarity between the individual genera. The method of dsRNA isolation using phenol-chloroform and cellulose was used for the detection of mycoviruses.
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Tool for Visualization of Microbiome Data
Mišáková, Silvia ; Martínek, Tomáš (referee) ; Smatana, Stanislav (advisor)
Táto práca sa zameriava na vytvorenie nového nástroja pre vizualizáciu mikrobiomových dát. Vytvorený nástroj používa pre redukciu dimenzií analýzu hlavných komponent (PCA) a analýzu hlavných súradníc (PCoA). V prípade výpočtu dištančnej matice sú použité metriky Bray-Curtis odlišnosť a UniFrac. Spracované dáta sú následne ofarbené na základe užívateľom zvolených metadát. Výsledky sú prezentované pomocou dvoch typov grafov. Prvý z nich je stĺpcový a zobrazuje podiel každej hlavnej zložky. Druhý, bodový graf, vizualizuje konečný výsledok požadovanej analýzy. V rámci práce bola pridaná možnosť stiahnuť si vypočítanú maticu a taktiež tabuľku prvých N hlavných zložiek vypočítaných danou analýzou.
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Štúdium variability sekvencie v géne MC1R u rôznych druhov zvierat
Dolnáková, Lenka
Colouration is an important phenotypic trait of animals and plays a substantial role in the characteristics of individual animal species. The MC1R gene has an essential role in colouration. This thesis is focused on the study of sequence variability in this gene and subsequent phylogram formation in selected species, which are: Bos Primigenius Taurus, Sus Scrofa, Equus Caballus and Canis Lupus Familiaris. There were custom primers designed in Oligo for the selected exon sequence. Based on se-quencing, known polymorphisms in Canis Lupus Familiaris and Equus Caballus were detected. In Canis Lupus Familiaris sequence, there was a 790 A>G polymorphism. All of N sequenced samples (N = 10) carried the E (790AA) allele. In Equus Caballus se-quence, there was a 901 C>T polymorphism, with representatives of all genotypes nEE(901CC) = 2, nEe(901CT) = 2, nee(901TT) = 6. The thesis also provides a comprehensive overview of the phylogenetic tree for-mation process. For phylogenetic analysis, there were added sequences from other ani-mal species, gained from freely available genomic databases. The reconstruction took place in the MEGA X program with selected distance and sign methods. Only nodes with bootstrap support ≥ 70 could be interpreted. JC69 and HKY85 models were cho-sen as substitution models. The choice of models was statistically supported by testing likelihood in the Model Generator with P < 0,0001 support. The trees obtained by par-ticular methods were compared by the Pearson correlation coefficient.
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Bioinformatic Tool for Classification of Bacteria into Taxonomic Categories Based on the Sequence of 16S rRNA Gene
Valešová, Nikola ; Hon, Jiří (referee) ; Smatana, Stanislav (advisor)
Tato práce se zabývá problematikou automatizované klasifikace a rozpoznávání bakterií po získání jejich DNA procesem sekvenování. V rámci této práce je navržena a popsána nová metoda klasifikace založená na základě segmentu 16S rRNA. Představený princip je vytvořen podle stromové struktury taxonomických kategorií a používá známé algoritmy strojového učení pro klasifikaci bakterií do jedné ze tříd na nižší taxonomické úrovni. Součástí práce je dále implementace popsaného algoritmu a vyhodnocení jeho přesnosti predikce. Přesnost klasifikace různých typů klasifikátorů a jejich nastavení je prozkoumána a je určeno nastavení, které dosahuje nejlepších výsledků. Přesnost implementovaného algoritmu je také porovnána s několika existujícími metodami. Během validace dosáhla implementovaná aplikace KTC více než 45% přesnosti při predikci rodu na datových sadách BLAST 16S i BLAST V4. Na závěr je zmíněno i několik možností vylepšení a rozšíření stávající implementace algoritmu.
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Search of the Bacterial Genome Descriptor
Vanek, Roman ; Martínek, Tomáš (referee) ; Burgetová, Ivana (advisor)
This bachelor thesis deals with the investigation of DNA sequences of bacterial genomes. The aim is to find out whether it is possible to determine on the basis of the nucleotide tuple frequencies from which bacteria specie the examined sequence originates. The investigation results were obtained by a tool whose implementation is also a part of the work. The output of this thesis are the experiments with nucleotide tuple frequencies based on statistical calculations and decision whether this approach is beneficial or not.
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Evolutionary models for evaluation of organisms relationship
Gregorová, Kateřina ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The work is focused on the study and description of evolutionary models for the evaluation of the evolutionary distances of DNA sequences and protein sequences in the amino acids and the codon representation. In the framework of this work was created a program that evaluates the genetic distance between DNA sequences and protein sequences for the use of some evolutionary models. The program calculates the genetic distance of the compared sequences and on the basis thereof renders the phylogenetic tree. This can be relatively easily and quickly evaluate the affinity of the organisms. For easy operation is part of the evaluation program also graphical user interface (GUI).
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Techniques for Multiple Sequence Alignments
Hrazdil, Jiří ; Martínek, Tomáš (referee) ; Burgetová, Ivana (advisor)
This thesis summarizes ways of representation of biological sequences and file formats used for sequence exchange and storage. Next part deals with techniques used for sequence pairwise alignment, followed by extension of these techniques to the problem of multiple sequence alignment. Additional methods are introduced, that are suboptimal, but on the other hand are able to compute results in reasonable time. Practical part of this thesis consists of implementing multiple sequence alignment application in Java programming language.
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Predicting the Effect of Amino Acid Substitutions on Protein Function Using MAPP Method
Pelikán, Ondřej ; Vogel, Ivan (referee) ; Bendl, Jaroslav (advisor)
This thesis discusses the issue of predicting the effect of amino acid substitutions on protein function using MAPP method. This method requires the multiple sequence alignment and phylogenetic tree constructed by third-party tools. Main goal of this thesis is to find the combination of suitable tools and their parameters to generate the inputs of MAPP method on the basis of analysis on one massively mutated protein. Then, the MAPP method is tested with chosen combination of parameters and tools on two large independent datasets and consequently is compared with the other tools focused on prediction of the effect of mutations. Apart from this the web interface for the MAPP method was created. This interface simplifies the use of the method since the user need not to install any tools or set any parameters.
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