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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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Spectrum sensing and multicarrier systems optimization for cognitive radio
Povalač, Karel ; Šimša, Jan (referee) ; Galajda,, Pavol (referee) ; Maršálek, Roman (advisor)
The doctoral thesis deals with spectrum sensing and subsequent use of the frequency spectrum by multicarrier communication system, which parameters are set on the basis of the optimization technique. Adaptation settings can be made with respect to several requirements as well as state and occupancy of individual communication channels. The system, which is characterized above is often referred as cognitive radio. Equipments operating on cognitive radio principles will be widely used in the near future, because of frequency spectrum limitation. One of the main contributions of the work is the novel usage of the Kolmogorov – Smirnov statistical test as an alternative detection of primary user signal presence. The new fitness function for Particle Swarm Optimization (PSO) has been introduced and the Error Vector Magnitude (EVM) parameter has been used in the adaptive greedy algorithm and PSO optimization. The dissertation thesis also incorporates information about the reliability of the frequency spectrum sensing in the modified greedy algorithm. The proposed methods are verified by the simulations and the frequency domain energy detection is implemented on the development board with FPGA.
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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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Spectrum sensing and multicarrier systems optimization for cognitive radio
Povalač, Karel ; Šimša, Jan (referee) ; Galajda,, Pavol (referee) ; Maršálek, Roman (advisor)
The doctoral thesis deals with spectrum sensing and subsequent use of the frequency spectrum by multicarrier communication system, which parameters are set on the basis of the optimization technique. Adaptation settings can be made with respect to several requirements as well as state and occupancy of individual communication channels. The system, which is characterized above is often referred as cognitive radio. Equipments operating on cognitive radio principles will be widely used in the near future, because of frequency spectrum limitation. One of the main contributions of the work is the novel usage of the Kolmogorov – Smirnov statistical test as an alternative detection of primary user signal presence. The new fitness function for Particle Swarm Optimization (PSO) has been introduced and the Error Vector Magnitude (EVM) parameter has been used in the adaptive greedy algorithm and PSO optimization. The dissertation thesis also incorporates information about the reliability of the frequency spectrum sensing in the modified greedy algorithm. The proposed methods are verified by the simulations and the frequency domain energy detection is implemented on the development board with FPGA.
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