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Analysis of local DNA structures
Kratochvíl, Jaromír ; Trenz, Oldřich (referee) ; Šťastný, Jiří (advisor)
This diploma thesis is focused on the description and implementation of the user interface for the analysis of local DNA structures as a web application in the Vue.js framework. The local structure can be described as an alternative DNA structure which arises in a specific DNA sequence that occurs in important regions of the genome. The first part of the thesis is theoretical and examines the field of DNA research and a description of selected technologies. The second part deals with the implementation and testing of the user interface on specific DNA sequences.
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Finding Approximate Palindromes in DNA Sequences
Remiáš, Richard ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
This work discusses problematics of exact and approximate palindrome searching. In relation with exact palindrome searching, native algorithm and algorithm using suffix trees, which construction is also analyzed, is presented. Approximate palindrome search is implemented with application of dynamic programming principles. The search itself is dividded into three parts: palidnrome search, result filter and reconstruction of palindromes. Each part is described by an algorithm and implemented in a program, contained in attachment.
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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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?Implementace algoritmu pro nalezení palindromu v DNA nukleotidových sekvencích
Diviš, Jan
This bachelor thesis focuses on the refactoring of the Palindrome Analyser tool’s code, whose algorithms and data structures are outdated and require updating. The aim of this work is to enhance the tool’s efficiency, reliability, and extendability through the use of new solutions and frameworks, as well as modernizing and supplementing missing tests to achieve proper functionality of the entire tool.
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Optimalizace algoritmu pro zjištění uspořádání nukleotidů v DNA
Studýnka, Petr
This bachelor thesis deals with rewriting the new version of the algorithm into a new one and visualization of Palindrom Analyzer, which is a part of DNA analyzer application. This tool is currently in working order, but it‘s source code is outdated, some it’s parts are missing tests, the algorithms used are not optimized and application backend part is tightly coupled with the application frontend.
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Analysis of local DNA structures
Kratochvíl, Jaromír ; Trenz, Oldřich (referee) ; Šťastný, Jiří (advisor)
This diploma thesis is focused on the description and implementation of the user interface for the analysis of local DNA structures as a web application in the Vue.js framework. The local structure can be described as an alternative DNA structure which arises in a specific DNA sequence that occurs in important regions of the genome. The first part of the thesis is theoretical and examines the field of DNA research and a description of selected technologies. The second part deals with the implementation and testing of the user interface on specific DNA sequences.
|
|
|
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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|
|
Finding Approximate Palindromes in DNA Sequences
Remiáš, Richard ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
This work discusses problematics of exact and approximate palindrome searching. In relation with exact palindrome searching, native algorithm and algorithm using suffix trees, which construction is also analyzed, is presented. Approximate palindrome search is implemented with application of dynamic programming principles. The search itself is dividded into three parts: palidnrome search, result filter and reconstruction of palindromes. Each part is described by an algorithm and implemented in a program, contained in attachment.
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