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Alignment of DNA Parts
Pejř, Václav ; Burgetová, Ivana (referee) ; Rozman, Jaroslav (advisor)
This thesis deals with finding the possibilities within the sphere of alignment of DNA sequences. Based on these findings, the best solution should be found with regard to the quickness of computation and quality of alignment. Following this I intend to implement and thus create a functioning program that will do the alignment. The thesis starts with introducing issues dealing with biology, DNA and genetics. The introduction is followed by a survey of algorithms that are used for alignment, their evaluation and selection of the most appropriate algorithm for the implementation. The thesis also focuses on the usage of parallel programming by means of OpenCL libraries. The alignment is being done above many sequences at the same time, so that the methods how this process can be done and how to reach the best results are being examined.
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DNA Fragmnent Assembly
Paulenda, Ján ; Jaša, Petr (referee) ; Burgetová, Ivana (advisor)
The main subject of this Bachelor's thesis is the DNA fragment assembly. The problem is transposed to finding a shortest superstring problem. Different assembly techniques and string aligning methods are introduced in the theoretical part. Programming language Perl, which was used to implement the assembly, is also widely mentioned, along with its features. Last part of the thesis involves tests' statistics of the final implemented solution.
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DNA Microarrays Data Analysis
Hebelka, Tomáš ; Jaša, Petr (referee) ; Burgetová, Ivana (advisor)
This work concerns with data analysis of DNA microarrays by using cluster analysis. It explains biological terms - gene expression and DNA microarray. Next, it contains mathematical and informatical description of clustering methods and describes a way to apply these methods to microarrays data. Next, the work contains implementation's detail of clustering methods k-means, DBSCAN and introduces an original clustering algorithm Strom++. Then, description of implementation and application manual follow. Finally, accomplished results are evaluated.
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Application for the Data Processing in the Area of Evolutionary Biology
Vogel, Ivan ; Burgetová, Ivana (referee) ; Očenášek, Pavel (advisor)
Phylogenetic tree inference is a very common method for visualising evolutionary relationships among species. This work focuses on explanation of mathematical theory behind molecular phylogenetics as well as design of a modified algorithm for phylogenetic tree inference based on intra-group analysis of nucleotide and amino acid sequences. Furthermore, it describes the object design and implementation of the proposed methods in Python language, as well as its integration into powerful bioinformatic portal. The proposed modified algorithmic solutions give better results comparing to standard methods, especially on the field of clustering of predefined groups. Finally, future work as well as an application of proposed methods to other fields of information technology are discussed.
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Parallel Multigenerative Cocke-Younger-Kasami-Based Parsing
Sopuch, Zbyněk ; Burgetová, Ivana (referee) ; Meduna, Alexandr (advisor)
We deal with text processing, pattern matching and syntax analysis every day, and new areas emerging. We can consider programming languages, communication protocols or a simple text as well-know examples. Therefore, we need new effective methods which fit into these areas. In this work, we explore the topics of parallel grammars, E0L-systems and multigenerative grammar systems. The goal is to improve the Cocke-Younger-Kasami algorithm and present a stronger algorithm of analysis.
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Analysis of DNA Structure Elements
Knytl, Marek ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
The aim of this master's thesis is the design and implementation of tool trackAnalysis for statistical analysis of DNA structure elements. The positions of individual elements in genome are obtained in the form of the track, and with these positions the tool performs a set of analyzes, including randomness test of track, test examining distances between track and genes, detection of clusters and overlaps. The indivudual tests results can be linked together. The results will be displayed in the form of a list, a graph or a new annotation track. An important part of this thesis is also testing the resulting tool on a set of real data.
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Delivery Information System
Petřík, Radek ; Stryka, Lukáš (referee) ; Burgetová, Ivana (advisor)
The field of this work was to create a web application easing shipper's and carrier's work with consignments. The purpouse of the application is evidence of packages combined with label printing. A prewiew of present-day web application development techniques is provided first. Recent package delivery systems are discussed then. The application specification is the next topic. Implementation process using C# ASP .NET and the results of this work is analyzed in the last chapters.
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A New Approach to LL and LR Parsing
Martiček, Štefan ; Burgetová, Ivana (referee) ; Meduna, Alexandr (advisor)
Cílem této práce je vytvořit nový efektivní způsob syntaktické analýzy propojením LL a LR přístupů. Pro demonstrační účely je zhotoven nový programovací jazyk podle vzoru programovacího jazyka PHP. Tento jazyk je rozdělen na části, kde pro každou část je použita ta nejvhodnejší ze zmíněných metod. Jednotlivé metody jsou zde podrobněji popsané v kontextu dvou typů přístupů. Jedním z nich je syntaktická analýza shora dolů a tím druhým opačná verze, syntaktická analýza zdola nahoru. Pro každou separovanou část je vytvořen samostatný syntaktický analyzátor. Táto práce poskytuje kompletní teoretický základ k sestrojení všech zde použitých syntaktických analyzátorů a rozkladových tabulek. Nakonec jsou sestrojené analyzátory společne propojeny, což je úspěšné zakončení praktické demonstrace naší metody. V závěru jsou diskutovány dosažené výsledky práce jako efektivnejší druh syntaktické analýzy, modularita přístupu a podobně. Je zde také diskutovaná použitelnost navržené metody za účelem zefektivnení vývoje a rychlosti překladu. Jako poslední jsou uvedeny náměty pro další výzkum v této oblasti.
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Application for the Data Processing in the Area of Evolutionary Biology
Radakovič, Lukáš ; Burgetová, Ivana (referee) ; Očenášek, Pavel (advisor)
This Bachelor’s thesis describes the design and implementation of the application that has the task to verify the accuracy of the algorithm. Purpose of the algorithm is to analyze mechanisms used in the creation of the phylogenetic tree. The application allows users to specify different parameters of phylogenetic tree, its generation and subsequent analysis using an algorithm. Results of the analysis are written to the output file, giving the user the option of setting file path. Studied algorithm correctly estimates the participation of specific mechanism in the tree formation. Estimates of the absolute and relative share of changes in chromosome number and genome size are less than accurate results.
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Clustering of Biological Sequences
Kubiš, Radim ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
One of the main reasons for protein clustering is prediction of structure, function and evolution. Many of current tools have disadvantage of high computational complexity due to all-to-all sequence alignment. If any tool works faster, it does not reach accuracy as other tools. Further disadvantage is processing on higher rate of similarity but homologous proteins can be similar with less identity. The process of clustering often ends when reach the condition which does not reflect sufficient quality of clusters. Master's thesis describes the design and implementation of new tool for clustering of protein sequences. New tool should not be computationally demanding but it should preserve required accuracy and produce better clusters. The thesis also describes testing of designed tool, evaluation of results and possibilities of its further development.
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