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Measurement of biological signals with Bipack system
Brudík, Vladislav ; Hlaváček, Antonín (referee) ; Valla, Martin (advisor)
This bachelor's thesis deals with questions of sensing electrical brain activity by electroencephalograph, and the data processing. Theoretical part is focused on brain, it's anatomy and functions. It also deals with biological signals, types of curves and systems used for measuring EEG curves. For purpose of signal processing it's been designed application software with GUI interface. This application software displays EEG curves, significant frequency ranges, frequency spectrum and filtered areas of characteristic waves.
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Mathematical analysis in mass spectrometry
Vlachová Hutová, Eliška ; Adam, Vojtěch (referee) ; Valla, Martin (advisor)
In this bachelor work, there is theoretically described the principle of mass spectometry and tandem mass spectometry, usage the method in practices and description of functionality of separate analysers. Next, there is also mentioned the description of mass spectrum and the algorithm to its analysis. Practical part of the work describes the creation of analytic tool to evaluate spectrum and following usage of this programming tool for the practical analysis of flavonoid compounds, concretely isoflavonoid.
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Determination genetics differencies using alignment signal of biological sequences DNA
Trněný, Ondřej ; Provazník, Ivo (referee) ; Valla, Martin (advisor)
Biological sequences are constantly evolving so there are mutations, deletions and inserts. Because of need to classify these sequences and determine degree of their similarity have been developed aligment methods. For example Dot matrix or algorithms like Needleman-Wunsch and Smith-Waterman used for global and local alignment. These methods can be considered as conservative and are limited because it is assumed that although there have been changes during evolution they still preserve small distance between similar regions. Therefore number of methods have been proposed to eliminate these limitations by comparing sequences without alignment. These methods for example Words in sequences, Euklidean distance or Universal sequence maps are designed to eliminate limitations of alignment using methods.
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Scoring Processing System for Protein Identification in Tandem Mass Spectrometry
Valla, Martin ; Svobodová-Vařeková, Radka (referee) ; Provazník, Ivo (advisor)
The goal of my diploma thesis was finding a suitable method for unifying score values from various protein identification search tools in MS/MS mass spectrometry into one single score value. Data coming from the output of mass spectrometer are processed in two independent search tools Mascot and X!Tandem. These were selected especially for their wide usage in proteomic labs. Both results are evaluated through newly designed function and unified by single valued score clearly identifying found proteins. Newly designed scoring value is called Matascore and function producing this score was implemented in MATLAB. Function and its results were successfully tested by real data available in public databases on the Internet.
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Measurent and analysis of genomic signal Solanum tuberosum.
Štekovič, Michal ; Hubálek, Jaromír (referee) ; Valla, Martin (advisor)
This thesis describes the basic methods for measuring and analyzing DNA. The first part covers the description of the DNA. The next section is devoted to the principle of obtaining DNA from the sample, its isolation and purification. Describes the apparatus which is necessary to measure and analyze. In the final section is devoted adsorptive voltammetry method, evaluation of measured results and data processing assistance program MATLAB.
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Explantation and analysis of plants
Kašpar, Blahoslav ; Babula,, Petr (referee) ; Valla, Martin (advisor)
The bachelor thesis is focused on the study of antioxidants and detection methods of their antioxidant activity. Antioxidants are substances able to scavenge the activity of oxygen radicals. This ability protects critical cellular structures from oxidation. In nature, plants belong to the important sources of antioxidants. In this thesis we are specifically focused on the detection of antioxidant activity of Japanese knotweed extracts using FRAP (“Ferric Reducing Antioxidant Power”) with automatic UV-Vis spectrometer. The data obtained were treated with the mathematical program developed in MATLAB.
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mRNA isolation of plants
Janíček, Zdeněk ; Hubálek, Jaromír (referee) ; Valla, Martin (advisor)
The bachelor thesis includes the information about different methods of the isolation of nucleic acids and focuses on the method which allows isolating of nucleic acids from Chinese lantern plant using paramagnetic particles. It includes the information about the best conditions for gaining sufficient amount of nucleic acid. The emphasis is put on the apparatus which is used for automated pipetting. The aim is to create a program for automated isolation of nucleic acids using paramagnetic particles.
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Representation and processing of genomic signals
Pitner, Vít ; Harabiš, Vratislav (referee) ; Valla, Martin (advisor)
This project deals with methods of representation and processing of genomic signals. The first part of this thesis describe linear expression of the sequence and statistical description of the sequence. For this purpose was used the real data, retrieved from public database, specifically the gene sequence of human chromosome Y. In the second part of the thesis are explained some methods of processing and representation of genomic signals. The following part describes a program designed for the processing sequence and is tested for short genomic sequences retrieved from public databases.
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Fractal of DNA sequence data
Nedvěd, Jiří ; Čech, Petr (referee) ; Valla, Martin (advisor)
This project is looking for fractal structury in DNA sequence data, which be maped in square ACGT. First, this project is introduced in problematics of fractals and targeted on making of Sierpinski gasket. Second, the project is introduced in DNA and DNA sequence. Next is sketched now known fractal’s structures in DNA sequence data or fractal’s structure closed DNA sequence. Then will changed metod chaos game of Sierpinski gasket to square ACGT, in where will drawen map of DNA sequences. Next, these pictures will processed by Box Counting Method and Power Spectrum Method.
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Processing of fractal genomic signals
Nedvěd, Jiří ; Provazník, Ivo (referee) ; Valla, Martin (advisor)
This diploma project is showen possibilities in classification of genomic sequences with CGR and FCGR methods in pictures. From this picture is computed classificator with BCM. Next here is written about the programme and its opportunities for classification. In the end is compared many of sequences computed in different options of programme.
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