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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.
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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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Identification of the Protein Tunnels Using Molecular Dynamics
Kohout, Petr ; Martínek, Tomáš (referee) ; Musil, Miloš (advisor)
This thesis focuses on the analysis of protein structures. The aim is to design Caver Web 2.0 -- a new version of the web application that integrates additional scientific tools and allows users to go through a complicated workflow to provide relevant results without the need for a deeper knowledge of the integrated tools. Everything will be delivered through a simple and interactive user interface. The application extends the original Caver Web 1.0 application with new features. Caver Web 1.0 is a web server suitable for identifying protein tunnels and channels for which it allows to run ligand transport analyses. The program is characterized by an intuitive and user-friendly interface with minimum required input from the user. The server is suitable for researchers without advanced bioinformatics or technical knowledge. Its current version is well established and highly used in the scientific community (35,000 completed calculations in two years of operation). The most significant limitation of the current version is the ability to analyze only static structure, which often provides an incomplete biological picture. Therefore, it was decided to extend the tool to calculate molecular dynamics to provide a comprehensive picture of protein structure changes.
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Database System for Biological Data Management
Drlík, Radovan ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This thesis describes the problems of storage and management of biological data, particularly of Haloalkane Dehalogenase enzymes. Furthermore, the thesis aims at project HADES (HAloalkane DEhalogenase databaSe) initiated by protein engineering group of Loschmidt Laboratories, Masaryk University in Brno. This is a project whose main goal is simply to store, preserve and display a wide variety of proteins data. The result of this work is a flexible database system allowing easy extensibility and maintainability, which is built on technologies Apache, PostgreSQL and PHP using the Zend Framework.
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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.
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Development of Meta-Server for Prediction of Mutations Effects on Protein Function
Lisák, Peter ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This bachelor thesis deals with analysis of genomic data, more specifically prediction of effects of mutations on protein function using a protein sequence or tertiary structure. The theoretical introduction describes the basics of genetics and bioinformatics and is followed by description of selected prediction tools such as SIFT, MAPP and AUTO-MUTE. A unified interface for work with different tools is proposed in the thesis. The meta-server interface allows running a computation and collecting results from one site. meta-server combines results of implemented tools and provides a consensual prediction, which is expected to be more accurate than the results from individual tools. Finally, testing of meta-server on the real data and comparisons of predictions with the experimentally obtained results are presented.
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Search of Related Enzymes
Borko, Simeon ; Smatana, Stanislav (referee) ; Hon, Jiří (advisor)
Millions of new proteins discovered each year cannot be characterized by classical biochemical methods due to their demands of time and cost. Among the unexplored proteins, there may be enzymes useful in both industry and academy, mostly for ecological production of chemical compounds. The result of the thesis is a web application which, based on the input proteins, searches the database for similar proteins. The proteins are filtered using essential residues of the input proteins and marked as putative biocatalysts. Finally, the proteins are annotated so that the user can make an informed decision about which proteins to select for experimental laboratory verification. The developed tool facilitates multi-step analysis and recommends proteins for experimental verification of their enzymatic function. The web interface is freely available at https://loschmidt.chemi.muni.cz/enzymeminer/. The tool was published in the international journal Nucleic Acids Research.
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The Application of Variational Autoencoders for Ancestral Sequence Reconstruction
Kohout, Pavel ; Martínek, Tomáš (referee) ; Musil, Miloš (advisor)
Protein engineering is an interdisciplinary science concerned with the design of improved proteins. A successful method used to design more stable and active proteins is ancestral sequence reconstruction. This method explores the evolutionary relationships between existing proteins and uses phylogenetic trees to generate their evolutionary ancestors, which often exhibit the desired improved properties. Therefore, new and more robust methods using mathematical models together with huge amounts of sequence data could become a powerful tool for protein engineering. This thesis explores the use of variational autoencoders as an alternative approach to ancestral sequence design compared to conventional methods using phylogenetic trees. Experiments were performed to optimize the architecture and statistical methods were proposed to evaluate the quality of the models and the sequences generated. At the same time, robustness tests of the whole method were performed and strategies for ancestral sequence generation were proposed and implemented.
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Detection of Related Proteins with Modified Function
Hon, Jiří ; Bendl, Jaroslav (referee) ; Martínek, Tomáš (advisor)
Protein engineering is a young dynamic discipline with great amount of potential practical applications. However, its success is primarily based on perfect knowledge and usage of all existing information about protein function and structure. To achieve that, protein engineering is supported by plenty of bioinformatic tools and analysis. The goal of this project is to create a new tool for protein engineering that would enable researchers to identificate related proteins with modified function in still growing biological databases. The tool is designed as an automated workflow of existing bioinformatic analyses that leads to identification of proteins with the same type of enzymatic function, but with slightly modified properties - primarily in terms of selectivity, reaction speed and stability.
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