1,720,980 research outputs found
Prediction of Quadruplex Structure
No full textThis master's thesis focuses on search and structure prediction of quadruplexes in DNA sequences. Thesis also explains related terms that are important for understanding the function, properties and geometry of quadruplexes. Thesis describe physico-chemical and computational current methods, which possible to discover and structure prediction. This paper also explain the principle of molecular modelling, which was used in the final application. Design and implementation of the final algorithm are also part of this thesis
Acceleration of Algorithms for Triplex Detection in DNA Sequences
No full textTriplex forms of DNA act as main factors of some important cell functions. However, their positions within genome and their effect on cell functions are not known well. Triplex search algorithms often don't consider many of triplexs features and the possibility of occurrence of errors. In the other hand the complexity of full featured algorithms is extremely high. This paper shows the way to speed up the algorithm that considers all known triplex features. Parallel aproach allows due to CUDA technology acceleration up to 50
Prediction of Quadruplex Structure
No full textThis master's thesis focuses on search and structure prediction of quadruplexes in DNA sequences. Thesis also explains related terms that are important for understanding the function, properties and geometry of quadruplexes. Thesis describe physico-chemical and computational current methods, which possible to discover and structure prediction. This paper also explain the principle of molecular modelling, which was used in the final application. Design and implementation of the final algorithm are also part of this thesis
Acceleration of Algorithms for Triplex Detection in DNA Sequences
No full textTriplexní formy DNA mají vliv na některé základní buněčné funkce. Informace o jejich umístění v genomech a všech vlivech na funkce organismu přesto nejsou známy. Většina algoritmů pro hledání triplexů neuvažuje důležité vlastnosti a možnost výskytu chyb. Komplexní algoritmy jsou velmi výpočetně náročné. Tato práce navrhuje způsob urychlení algoritmu, který při hledání triplexů uvažuje všechny známé informace. Akcelerací algoritmu pomocí paralelního zpracování technologií CUDA bylo dosaženo až 50-ti násobného zrychlení.Triplex forms of DNA act as main factors of some important cell functions. However, their positions within genome and their effect on cell functions are not known well. Triplex search algorithms often don't consider many of triplexs features and the possibility of occurrence of errors. In the other hand the complexity of full featured algorithms is extremely high. This paper shows the way to speed up the algorithm that considers all known triplex features. Parallel aproach allows due to CUDA technology acceleration up to 50.
Reconstruction of Repetitive DNA Segments
No full textHlavní motivací diplomové práce bylo najít vhodný algoritmus, který by vytvořil grafovou reprezentaci NGS sekvenačních dat v lineárním čase. Zvolenou metodou pro reprezentaci je de Bruijnův graf. V další části práce byl navrhnut nástroj, který je schopen transformovat graf do přijatelné podoby pro vykreslování, a dále je schopen odstraňovat chyby, které vznikají při konstrukci grafu. Cílem práce je vytvořit nástroj, který rekonstruuje repetitivní segmenty v DNA. Implementovaný nástroj byl otestován a je schopen identifikovat opakující se segmenty, určit jejich typy, vizualizovat je a sestavit jejich sekvenci na jednodušších genomech s velkou přesnotí. Při použití složitějších genomů, nástroj nalezne pouze fragmenty repetitivních segmentů
Quadruplex Detection in DNA Sequences
No full textThis master's thesis focuses on search for sequences potentially forming quadruplexes in DNA sequences, their visualization and filtration. For this purpose a web application was created in cooperation with the Institute of biophysics of Academy of science of Czech republic. This application uses a newly created algorithm able to find all possible formations of quadruplex within given input sequence. Design and implementation of this algorithm are also part of this thesis
Approximate Palindrome Detection in DNA Sequences
No full textThis work deals with conception and implemetation of tools for finding approximate palindromes in DNA sequences. The work focuses on the description of DNA structure, and on the function of palindromes in DNA sequences, and on the description of methods for finding approximate palindromes. Main part of thesis is focused on conclusion and description of implementation approximate palidromes finding tool
Quadruplex Detection in DNA Sequences
No full textTato diplomová práce se zabývá vyhledáváním, vizualizací a filtrací sekvencí potenciálně tvořících kvadruplexy v sekvencích DNA. Ve spolupráci s Biofyzikálním ústavem AV ČR byla za tímto účelem vytvořena webová aplikace, která využívá nový algoritmus pro hledání všech možných umístění kvadruplexů v rámci zadané sekvence. Návrh a implementace tohoto algoritmu jsou také součástí této práce.This master's thesis focuses on search for sequences potentially forming quadruplexes in DNA sequences, their visualization and filtration. For this purpose a web application was created in cooperation with the Institute of biophysics of Academy of science of Czech republic. This application uses a newly created algorithm able to find all possible formations of quadruplex within given input sequence. Design and implementation of this algorithm are also part of this thesis.
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