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Classification of cardiac cycles
Lorenc, Patrik ; Škutková, Helena (referee) ; Vítek, Martin (advisor)
This work deals with the classification of cardiac cycles, which uses a method of dynamic time warping and cluster analysis. Method of dynamic time warping is among the elderly, but for its simplicity compared to others is still very much used, and also achieved good results in practice. Cluster analysis is used in many fields such as marketing or just for biological signals. The aim of this work is a general introduction to the ECG signal and the method and implementation of dynamic time warping algorithm. Subsequently, cluster analysis and finally the creation of the user interface for the algorithms.
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Dependence of derived fibrinogen on values of DH from APTT and QUICK(PT) methods
Klus, Michal ; Zapletal,, Ondřej (referee) ; Škutková, Helena (advisor)
Hemocoagulation, blood coagulation, is an important indicator of hemostatic balance in the human body. There are many ways how to investigate blood clotting. In practice, next to the tests investigating time of coagulation cascade from view of internal way (APTT – activated partial tromboplastin time) and external way (PT – prothrombin time) is often used determining of fibrinogen concentration by Clauss method. Derived fibrinogen method determined fibrinogen concentration, too, by subtracting form the clotting curve in PT test. The reaction for Clauss method is not necessary here. Derived fibrinogen is not used much in practice. This is the reason, why the thesis related to this project will try to find relationship between concentration of fibrinogen and standard tests APTT and PT. Clinical data will be used for this.
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The use of genomic signal compression for classification and identification of organisms
Sedlář, Karel ; Vítek, Martin (referee) ; Škutková, Helena (advisor)
Modern classification of organisms is performed on molecular data. These methods rely on multiple alignment of sequences of characters which make them computationally demanding. Only small parts of genomes can be compared in reasonable time. In this paper, the novel algorithm based on conversion of the whole genome sequences to cumulative phase signals is presented. Dyadic wavelet transform is used for lossy compression of signals by redundant frequency bands elimination. Signal classification is then performed as a cluster analysis using Euclidian metrics where multiple alignment is replaced by dynamic time warping.
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Statistic evaluation of phylogeny of biological sequences
Zembol, Filip ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
The topic of my diploma thesis is the statistical evaluation of biological sequences with the help of phylogenic trees. In the theoretical part we will create a literary recherche of estimation methodology concerning the course of phylogeny on the basis of the similarity of biological sequences (DNA and proteins) and we will focus on the inaccuracies of the estimation, their causes and the possibilities of their elimination. Afterwards, we will compare the methods for the statistical evaluation of the correctness of the course of phylogeny. In the practical part of the thesis we will suggest algorithms that will be used for testing the correctness of the phylogenic trees on the basis of bootstrapping, jackknifing, OTU jackknifing and PTP test which are able to the capture phylogenic tree with the method neighbor joining from the biological sequences in FASTA code. It is also possible to change the distance model and the substitution matrix. To be able to use these algorithms for the statistical support of phylogenic trees we have to verify their right function. This verification will be evaluated on the theoretical sequences of the amino acids. For the verification of the correct function of the algorithms, we will carry out single statistical tests on real 10 sequences of mammalian ubiquitin. These results will be analysed and appropriately discussed.
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Methods for multialignment of nucleotide sequences
Trněný, Ondřej ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
To be able to understand characteristics and purpose of biological sequences correctly, it is crucial to have a possibility to sort and compare them. Because of this need and to extend existing knowledge pool, numerous methods were proposed. Especially in field of multiple sequences alignment. Methods for multiple sequences alignment may provide various valuable information about sequences which failed to show enough similarity in pairwise alignment. According to this, several algorithms were implemented in various computer applications which provide a way to analyse huge sets of data. One of those, the progressive alignment algorithm, is implemented as a part of this thesis
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Fuzzy classification of DNA sequences
Těthal, Jiří ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The work deals with the fuzzy classification of DNA sequences. In the first part the theory summarized information about Fuzzy logic and methods of its use in the classification of biological sequence data. The second part is practically deal with the classification algorithm for assessing the similarity of sequences. Specifically, the dividing of coding and non-coding parts of the sequence and the use of fuzzy classification in DNA barcoding.
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Methods for phylogenetic supertree reconstruction
Jirásková, Kristýna ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
The phylogenetic reconstruction has noted great development in recent decades. The development of computers and device for sequencing biopolymers have been an enormous amount od phylogenetic data from different sources and different types. The scientists are trying to reconstruct a comlet tree of life from these data. The phylogenetic supertree are theoretically this option because a supertree alow a combination of all information gathered so far – in contras to the phylogenetic trees. This thesis present the method of reconstruction supertrees using average konsensus method.
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Mutual similarity of aminoacid sequences in different organisms
Vysoudil, Ladislav ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
The aim of this semestral project is to try to study and describe work with sequences of proteins of different organisms, namely above all alligment sequences and evaluation of similarities of sequences. At the beginning of this work we deal with biochemistry of proteins, their constitution and structure. Further text go on with theory for work with sequential data, global, local and multiple assignment. At the last part we investigate possibilities of programme Matlab for aforesaid assignment.
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Acoustic generator for evoked potentials stimulation
Škutková, Helena ; Rampl, Ivan (referee) ; Chmelař, Milan (advisor)
Evoked potentials are electric brain response to external stimulus. They are important diagnostic no visual method in neurology. For their excitation use of different of kinds stimulation, most often: visual, auditory, somatosenzory, olfactory and gustatory. Evoked potentials are objective method for measurement sense perception. This master’s thesis is specialized to auditory evoked potentials and design acoustic generator for their stimulation. Auditory evoked potentials are primary used for objective audiometry, but they have another usage. In the first place, application is specialized on health sector. The aim of this master’s thesis is compact specified medical requirements with available technical resources.
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