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Approximate String Matching Algorithm Implementation in FPGA
Pařenica, Martin ; Martínek, Tomáš (referee) ; Fučík, Otto (advisor)
This paper describes sequence alignment algorithms of nucleotide sequences. There are described pairwise alignment algorithms using database search or dynamic programming. Then in the paper is description of dynamic programming for multiple sequences and algorithm that builds phylogenetic trees. At the end of the first part of the paper is the description of technology FPGA. In the second part that is more practical is described implemntation of the choosen one algorithm. This part includes also examples of some multiple alignments.
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Clustering of Protein Sequences Based on Primary Structure of Proteins
Jurásek, Petr ; Stryka, Lukáš (referee) ; Burgetová, Ivana (advisor)
This master's thesis consider clustering of protein sequences based on primary structure of proteins. Studies the protein sequences from they primary structure. Describes methods for similarities in the amino acid sequences of proteins, cluster analysis and clustering algorithms. This thesis presents concept of distance function based on similarity of protein sequences and implements clustering algorithms ANGES, k-means, k-medoids in Python programming language.
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Approximate Palindrome Detection in DNA Sequences
Divila, Jaroslav ; Lexa, Matej (referee) ; Martínek, Tomáš (advisor)
This 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.
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Query-by-Example Keyword Spotting
Skácel, Miroslav ; Hannemann, Mirko (referee) ; Szőke, Igor (advisor)
Tato diplomová práce se zabývá moderními přístupy detekce klíčových slov a detekce frází v řečových datech. V úvodní části je seznámení s problematikou a teoretický popis metod pro detekci. Následuje popis reprezentace vstupních datových sad použitých při experimentech a evaluaci. Dále jsou uvedeny metody pro detekci klíčových slov definovaných vzorem. Následně jsou popsány evaluační metody a techniky použité pro skórování. Po provedení experimentů na datových sadách a po evaluaci jsou diskutovány výsledky. V dalším kroku jsou navrženy a poté implementovány moderní postupy vedoucí k vylepšení systému pro detekci a opět je provedena evaluace a diskuze dosažených výsledků. V závěrečné části je práce zhodnocena a jsou zde navrženy další směy vývoje našeho systému. Příloha obsahuje manuál pro používání implementovaných skriptů.
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Program system for solving dynamic programming problems
Zetka, Petr ; Popovský, Vítězslav (referee) ; Dvořák, Jiří (advisor)
This work deals with building a program system for solving dynamic programming problems on a computer. The theoretical part describes dynamic programming as a tool used for optimizing multistage decision processes and dynamic programming problems implemented in the program system. The practical part describes the design and implementation of the program system and verification of its functionality.
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Robot path planning by means of dynamic programming
Stárek, Ivo ; Krček, Petr (referee) ; Dvořák, Jiří (advisor)
This work is dedicated to robot path planning with using principles of dynamic programing in discrete state space. Theoretical part is dedicated to actual situation in this field and to principle of applying Markov decission process to path planning. Practical part is dedicated to implementation of two algorithms based on MDP principles.
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Database of acoustic records
Terz, Marek ; Schimmel, Jiří (referee) ; Sysel, Petr (advisor)
The databsae of accoustical recordings is a web-based application, which is accessible with an usual web browser. There were used technologies, that are ussually used in web applications. This ensures, that the application is open for using by wide range of users. The application enables uploading WAWE files to the server and allows the user to add various description of the recordings. The application allows also comparing the quality of recordings, which were processed with some method for highlighting the accoustical signal from noise. This function is established by listening tests, which are open for every user, who wants to join the tests.
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Solving of integer problems by dynamic programming
Polonyankina, Tatiana ; Kalčevová, Jana (advisor) ; Lagová, Milada (referee)
Optimalization problems with integer requirements on the variables occurs in real life very often. Unfortunately, finding optimal solutions to such problems are often numerically very difficukt. The work describes several possible algorithms for solving linear integer problems. The reader is also familiarized with the method of dynamic programming and the principle of optimality. This is demonstrated in a practical example of a knapsack model where the calculation is done using tables. The goal of this work is to apply the knowledge from the application of dynamic programming on a typical linear integer problems, namely on the problem of material separation, and thus show the algorithm of calculating integer problems. Finding the optimal integer solution is accomplished in two ways: by the classical method of spreadsheet tables and by the simplified method of using Lagrange multipliers. In the conclusion there are summarized the advantages and disadvantages of solving technic.
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