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Direct assembly of genome signals from nanopore sequencing
Karmazinová, Inna ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
The aim of this bachelor thesis is to search for overlaps between signals from nanopore sequencing using MinION device version R9. The theoretical part deals with methods used for genome assembly - greedy algorithm, overlap-layout-consensus (OLC) and de Bruijn graphs. Oxford Nanopore Technologies introduced the MinION device, which simplifies sequencing using the current change, which occurs while the DNA is passing through the nanopore. The error rate of the device is still high, the accuracy problem occurs during the base-calling. Using the difference signal, possibly also the dynamic time warping, it is possible to find overlaps between the individual signals. Signal analysis and genome assembly using the MinION signal could provide better accuracy.
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Traveling Salesman Problem: Parallel Methods Using SMP (Threads)
Weigner, Martin ; Jaroš, Jiří (referee) ; Kašpárek, Tomáš (advisor)
This thesis is focused on solving the problem of traveling salesman. At first, the problem is solved by serial access at four algorithms. There are two of them chosen and transferred to parallel access. In the end there are summarized observations about different parameters of both access. This thesis also introduces questions of programming parallel applications with threads to the reader.
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Travelling Salesman Problem
Řezníček, Jan ; Zbořil, František (referee) ; Zbořil, František (advisor)
The work focuses on implementing algorithms that solve the Traveling Salesman Problem. It also includes a user interface with a map for importing locations. The main algorithms that are part of the work are ACO and an algorithm that I have devised and implemented. ACO optimization improves results, such as setting initial pheromone levels using the nearest neighbor algorithm. My algorithm works on the principle of gradually improving the path.
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Direct assembly of genome signals from nanopore sequencing
Karmazinová, Inna ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
The aim of this bachelor thesis is to search for overlaps between signals from nanopore sequencing using MinION device version R9. The theoretical part deals with methods used for genome assembly - greedy algorithm, overlap-layout-consensus (OLC) and de Bruijn graphs. Oxford Nanopore Technologies introduced the MinION device, which simplifies sequencing using the current change, which occurs while the DNA is passing through the nanopore. The error rate of the device is still high, the accuracy problem occurs during the base-calling. Using the difference signal, possibly also the dynamic time warping, it is possible to find overlaps between the individual signals. Signal analysis and genome assembly using the MinION signal could provide better accuracy.
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Combinatorial problems with coins
Hamáček, Jan ; Slavík, Antonín (advisor) ; Fiala, Jiří (referee)
Práce se zabývá otázkami reprezentace zvolené částky pomocí libovolného množství mincí předep- saného typu. V první kapitole odvozujeme vzorce pro počet nereprezentovatelných částek a hodnotu největší nereprezentovatelné částky pro dvoumincové systémy. Dále ukazujeme grafový algoritmus pro výpočet Frobeniova čísla a d·kaz NP-úplnosti rozhodovacího problému reprezentovatelnosti zvolené částky v systému s více mincemi. V druhé kapitole se zabýváme výpočtem počtu reprezentací částky zvláš' v systémech o dvou nebo více mincích. Ve třetí kapitole se věnujeme otázce, zda lze ve zvoleném systému mincí použít hladový algoritmus pro nalezení reprezentace částky pomocí nejmenšího možného množství mincí. Poslední kapitola obsahuje sbírku řešených logických úloh o mincích. 1
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Traveling Salesman Problem: Parallel Methods Using SMP (Threads)
Weigner, Martin ; Jaroš, Jiří (referee) ; Kašpárek, Tomáš (advisor)
This thesis is focused on solving the problem of traveling salesman. At first, the problem is solved by serial access at four algorithms. There are two of them chosen and transferred to parallel access. In the end there are summarized observations about different parameters of both access. This thesis also introduces questions of programming parallel applications with threads to the reader.
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