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Mapping of motion artefact in fMRI
Nováková, Marie ; Kremláček, Jan (referee) ; Jan, Jiří (advisor)
This thesis summarizes a theory of magnetic resonance and the method of functional magnetic resonance. It is focused on the influence of motion artifacts and image preprocessing methods, especially realign. It deals with the possibility of using movement parameters obtained in the process of alignment of functional scans to create maps that show the expression of motion artifacts. In this thesis, three different methods were designed, implemented a tested. These methods lead to the creation of probability, power and statistical group maps showing areas typically affected by movement artifacts.
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Text to Audio Alignment
Šuba, Adam ; Hradiš, Michal (referee) ; Szőke, Igor (advisor)
This bachelor thesis studies a tool for automatic text to audio alignment at the level of single phonemes and graphemes. It also discusses possible techniques used in alignment and possible limitations and difficulties that need to be taken into account. Studied tool uses approach based on grapheme-to-phoneme conversion using joint-sequence models. Data used in experiments are TV broadcast recordings from Multi-Genre Broadcast Challenge 2015.
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Application for Alignment of DNA Parts
Kašpárek, Tomáš ; Žák, Jakub (referee) ; Rozman, Jaroslav (advisor)
This thesis deals with DNA sequences alignment methods with focus on execution speed of given task and its optimality. The outcome of this thesis results in multiple programs, which presents DNA alignment algorithms and their versions programmed with OpenCL libraries, which are optimized on calculation rate. Text of this thesis apprises reader with DNA alignment problematic and its importance in biology. Further, algorithms for DNA alignment and options of their speed-up using libraries like CUDA or OpenCL are presented.
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Automatic rotational alignment of head CT scans
Karmazinová, Inna ; Kolář, Radim (referee) ; Jakubíček, Roman (advisor)
The aim of this thesis is automatic alignment of head CT scan. Currently, the alignment is performed manually by an expert, however this process is time consuming. Therefore, methods for automatization of this process are being developed. Two algorithms for alignment in axial and coronal plane were designed based on bilateral symmetry of head. Following an algorithm for alignment in sagittal plane which uses CG-TOB reference line for rotation angle detection. Algorithms were implemented in MATLAB and tested and validated using a database of manually annotated head CT scans.
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Genomic Data Mining Techniques
Jaša, Petr ; Křivka, Zbyněk (referee) ; Burgetová, Ivana (advisor)
First of all, this thesis sets itself a goal to introduce some common technics for datamining in genomics and as a next step to implement own algorithm like algorithm BLAST. In the concrete, this work is pointed to sequences of DNA. The DNA sequence contains in itself genetic information, which is template for living organism. For explanation this information can be used number of technics. This paper describes algorithm Fasta and algorithms from BLAST family. With these algorithms, it is possible to gain a lot of important information even about such DNA sequences, where only primary structure is known. Principle of these algorithms is based on alignments of one query sequence, which we want to obtain some information from, with many sequences stored in database. According to result alignment, it is possible to determine many features of the query sequence.
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Protein Structure Prediction
Tuček, Jaroslav ; Martínek, Tomáš (referee) ; Burgetová, Ivana (advisor)
This work describes the three dimensional structure of protein molecules and biological databases used to store information about this structure or its hierarchical classification. Current methods of computational structure prediction are overviewed with an emphasis on comparative modeling. This particular method is also implemented in a proof-of-concept program and finally, the implementation is analysed.
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Automatic Creation of Dictionaries from Translations
Sumbalová, Lenka ; Kouřil, Jan (referee) ; Smrž, Pavel (advisor)
The aim of this bachelor thesis was to make a system for automatic creation of dictionaries from translations. It describes the implementation of a system that generates Czech-English dictionary from the aligned parallel corpus and summarizes the results. It also analyzed CzEng parallel corpus, which was used as the data source for dictionaries and explainS the theoretical concepts related to this topic.
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Graphical representation of DNA and protein sequences
Pražák, Ondřej ; Kolářová, Jana (referee) ; Maděránková, Denisa (advisor)
Modification of DNA sequences and their suitable representation is important part of analysis, comparison and another processing. Goal of this paper is finding of suitable methods for representation of genomic and proteomic sequences. Because there is great number of metods, this paper will introduce only some of them. All selected methods, are described in the first part of this paper and they were programed in Matlab. Selected methods are illustrated on coding sequences of the first exon of the b-globin gene of 11 different species. Results are compared withresults from the original papers. Some methods are capable of another processing like cluster analysis. Output of this paper is comparison of results, gained from different methods, and finding the most suitable one.
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Hardware Acceleration of Algorithms for Approximate String Matching
Nosek, Ondřej ; Kořenek, Jan (referee) ; Martínek, Tomáš (advisor)
Methods for aproximate string matching of various sequences used in bioinformatics are crucial part of development in this branch. Tasks are of very large time complexity and therefore we want create a hardware platform for acceleration of these computations. Goal of this work is to design a generalized architecture based on FPGA technology, which can work with various types of sequences. Designed acceleration card will use especially dynamic algorithms like Needleman-Wunsch and Smith-Waterman.
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