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Study of Optical and Electrical Properties of Biomaterials
Flimelová, Miroslava ; Táborský, Petr (referee) ; Drbohlavová, Jana (referee) ; Weiter, Martin (advisor)
Studium nových materiálů potenciálně využitelných pro organickou elektroniku a fotoniku získává velmi důležitý význam z hlediska ekologie. Tato práce je zaměřena na studium vlastností biologických materiálů, které by našly uplatnění v aplikační sféře. Zájem o znalosti v oblasti základních a pokročilých vlastností organických a biologických materiálů, které mohou být potenciálně využity v oblasti organické elektroniky a fotoniky přináší nové otázky, které mohou přispět k rozvoji této oblasti. Ke studiu základních procesů souvisejících s optickými a elektrickými vlastnostmi materiálů, jako je například přenos náboje, jsme využili různé techniky a metody charakterizace. První část práce je zaměřena na souhrn vlastností anorganických a organických materiálů umožňující jejich možné využití v organické elektronice a fotonice, druhá část práce poskytuje nejnovější přehled z oblasti pokročilých biologických materiálů a jejich vlastností související se záměrem této práce. Třetí část práce pak shrnuje experimentální metody a shrnuje získané výsledky. Nakonec je diskutován vztah mezi pozorovanými jevy a strukturou studovaných materiálů na molekulární úrovni.
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Reconstruction of DNA Sequences Containing Repetitive Patterns
Dvořáček, Vojtěch ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
This bachelor thesis focuses on reconstruction of repetitive patterns in DNA sequences. Although it is motivated by need to create automated tool for telomere characterization in plant genomes, its goal is creating general solution of given problem. Suggested solution is based on k-mer analysis, which is alignment free method. Its greatest advantage lies in possibility to reconstruct repetitive patterns from NGS sequencing data. Within the scope of this work was designed and iplemented solution, which is able to automatically estiamte suitable parametres for k-mer analysis from input data and optimize them by local state space search method.
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Visualization of Transposons' Genomic Features
Nétková, Barbora ; Bendl, Jaroslav (referee) ; Vogel, Ivan (advisor)
This thesis deals with visualization of transposons' genomic features. The Genomic feature format (GFF) is an input file to visualisation. This type of file has strict definition and it is nowadays a de-facto standard format for genome description. Although there are several tools for GFF visualization, an open source application with advanced visualization features is missing. This work presents a design of such a tool. The application has a graphical user interface to simplify the user's work and combines the advantages of existing commercial products with free access. The application provides simple way to import user's biological data from a GFF file, creates hierarchical tree of individual elements including a detailed internal structure visualization in a subwindow.
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Visualization of DNA Secondary Structures in R/Bioconductor
Jaroš, Marta ; Bendl, Jaroslav (referee) ; Martínek, Tomáš (advisor)
This bachelors thesis deals with the visualization techniques of the secondary structures of DNA. It summarizes and discusses some of the current methods of visualization. It explains the problem and its importance from the standpoint of molecular biology. The main aim of the work is the design of a generic algorithm for visualization of secondary structures of DNA, specifically palindromes and triplexes, and its implementation into the environment R/Bioconductor. It focuses in particular on the area of 2D graphical imaging of these secondary structures of DNA. The result of the work is 2D visualization support for R/Bioconductors software packages which provide searching of the characteristic sequence of palindromes and triplexes in DNA sequences.
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Attributes Calculation for Prediction of Mutation Effect on Protein Function
Šinkora, Jan ; Filák, Jakub (referee) ; Jaša, Petr (advisor)
This thesis deals with issues of bioinformatics, machine learning, algorithms and data structures. The thesis is based on existing applications, Caver and Deleterious, developed by students from the Faculty of Informatics, Masaryk University and the Faculty of Information Technology, Brno University of Technology. The Deleterious framework calculates protein attributes that are important for the prediction of the effect of protein mutations on its function. Caver is a tool that finds tunnels in the 3-dimensional model of a protein. The goal of the thesis is to extend these applications by adding more attributes to the prediction process that could lead to improved prediction. The added attributes are related to detection and measurement of protein pockets.
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Gene Detection in DNA Sequences
Bahurek, Tomáš ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
This work is about gene detection in DNA sequencies. It explains how the information in DNA is stored, shows preview of various gene prediction methods, describes picked methods and results of testing those methods on real data (genome of bacteria E. Coli K12), compares efficiency of methods with various paramaters and efficiency between methods.
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Gene Searching - Web Application
Stiborová, Lucie ; Koutný, Jiří (referee) ; Burgetová, Ivana (advisor)
The aim of my Bachelor's Thesis is to create a user interface and to implement the web application with the genes' searching. This is the educational application when each user has a possibility of entering own nucleotide sequences or selecting a redefined chain. This application has to be able to read, process and decide on the existence of a potential gene. On the base of this simple statistic method the result is given back to the user.
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Web Application for Bioinformatics Education - Genetic Code
Kilián, Martin ; Martínek, Tomáš (referee) ; Burgetová, Ivana (advisor)
This thesis briefly describes basic informations in moleculary biology. Thesis deals with a transfer of information from DNA into RNA through uprotein, are also briefly described the methods and algorithms dealing with the detection of genome. The larger part deals with the recognition cue coded signals and determination of sequences and their subsequent transcription and translation, which demonstration program was needed to create. The final result is s web application as the education system.
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Analysis of Genomic Data with the Assistance of Algorithm BLAST
Křížová, Martina ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This Bachelor Thesis describes analysis of genomic data with assistance of algorithm BLAST. In theoretic part, it describes genomes, their importance and structure. In this thesis, you can find a description of algorithm BLAST, Smith-Waterman and Needleman-Wunsch and with algorithm BLAST connected Karlin-Altschul statistics. This thesis is discussing types of databases such as spatial, deductive and relational which store genomic data. Second part is concerned with design and implementation of application which use mentioned algorithm and database Oracle 10g R2. Testing and confrontation output of algorithm is also a part of this work.
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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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