National Repository of Grey Literature 74 records found  beginprevious49 - 58nextend  jump to record: Search took 0.00 seconds. 
Numerical methods for classification of metagenomic data
Vaněčková, Tereza ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
This thesis deals with metagenomics and numerical methods for classification of metagenomic data. Review of alignment-free methods based on nucleotide word frequency is provided as they appear to be effective for processing of metagenomic sequence reads produced by next-generation sequencing technologies. To evaluate these methods, selected features based on k-mer analysis were tested on simulated dataset of metagenomic sequence reads. Then the data in original data space were enrolled for hierarchical clustering and PCA processed data were clustered by K-means algorithm. Analysis was performed for different lengths of nucleotide words and evaluated in terms of classification accuracy.
Use of molecular-genetic methods for research of colorectal carcinoma
Janáková, Tereza ; Škutková, Helena (referee) ; Provazník, Ivo (advisor)
The aim of this bachelor work is to carry out statistical analysis of mutations in KRAS, BRAF and PIK3CA genes. Introductory part is focused on colorectal carcinoma in general. In following part of the work, we discuss genetics of tumors, description of KRAS, BRAF and PIK3CA genes, molecular-genetic analytical methods, widely used in genetics, especially PCR. Further detection of mutations is described. In the next part of the work, we propose a method for detection of mutations in KRAS, BRAF and PIK3CA genes, which consist in using PCR and commercial kits. The following chapter "Results of Analysis of mutations" contains detailed grafical presentation of mutations. Frequencies of mutations were compared with published data and with data from laboratories in Pilsen and Prague. In the end of the bachalor work, there is summary of results and their possible benefit.
Distance methods for reconstruction of phylogenetic trees
Šudák, Vítězslav ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
Thesis „Distance methods for reconstruction phylogenetic trees“ summarizes notes about methods for calculating evolutionary distances from aligned nucleotide, eminoacid or codon sequences. Then using these distances in methods for reconstructing phylogenetic trees from matrixes made of these distances. Aim is to create these method as a functional scripts in MATLAB software and appliance these method on real sequences downloaded from public databanks on internet in FASTA format, and to create a thesis about hese methods and describe them and my results.
Evaluation of Organisms Relationship by Genomic Signal Processing
Škutková, Helena ; Tkacz, Ewaryst (referee) ; Schwarz,, Daniel (referee) ; Provazník, Ivo (advisor)
This dissertation deals with alternative techniques for analysis of genetic information of organisms. The theoretical part presents two different approaches for evaluation of relationship between organisms based on mutual similarity of genetic information contained in their DNA sequences. The first approach is currently standardized phylogenetics analysis of character based records of DNA sequences. Although this approach is computationally expensive due to the need of multiple sequence alignment, it allows evaluation of global and local similarity of DNA sequences. The second approach is represented by techniques for classification of DNA sequences in a form of numerical vectors representing characteristic features of their genetic information. These methods known as „alignment free“ allow fast evaluation of global similarity but cannot evaluate local changes. The new method presented in this dissertation combines the advantages of both approaches. It utilizes numerical representation similar to 1D digital signal, i.e. representation that contains specific trend along x-axis. The experimental part of dissertation deals with design of a set of appropriate tools for genomic signal processing to allow evaluation mutual similarity of taxonomically specific trends. On the basis of the mutual similarity of genomic signals, the classification in the form of dendrogram is applied. It corresponds to phylogenetic trees used in standard phylogenetics.
Protein calculator
Sedlo, Petr ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
This work is focussed on studying and analysis of protein qualities while using experimental methods which are next confronted with numerical analysis, which have been introduced by the expansion in computer engineering. Within that task I built up a program for calculation of isoelectric point and molecular mass of an entered chain of amino acids. The program will draw a graph of pH dependance of molecular charge in the wide range of pH values in accordance with the given criteria. We can gain results very quickly and easily in this way, however, these results are just a rough estimate. We´re assumed to be aware of this fact because incorrect use of that program where exact analysis is required would cause errors.
Predictive models in survival analysis
Hadwigerová, Michaela ; Vítek, Martin (referee) ; Škutková, Helena (advisor)
With ever-new methods of treatment in health care occures a requierement of comparing these new methods to the old methods in some effective way. This is particularly important for the further development of these methods. However, data that describe these facts could not be processed by normal procedures and therefore was in the field of statistics to create a new kind of methods. They are known as predictive models of survival analysis.
Bootstrap methods in phylogenetics
Sedlář, Karel ; Vohánka,, Jaroslav (referee) ; Škutková, Helena (advisor)
In recent decades, phylogenetic reconstruction has noted great development. It was achieved by using newly acquired molecular characteristics and processing that it began to be taken as an objective science. Rapid development showed that it is necessary to evaluate the results because new techniques provided phylograms from unreliable data. For these purposes, statistical sampling methods have been applied to the phylogeny, of which bootstrapping began later to dominate. However, it also has limitations, which should be considered during interpreting the results it provided to us. This work demonstrates by combining the principles of bootstrapping and consensus trees we can obtain phylograms with better properties than those of conventional phylograms.
Program for measuring response time to visual and auditory stimulation
Machatý, Jiří ; Škutková, Helena (referee) ; Sekora, Jiří (advisor)
The work was written in C + + whit qt toolkit: a "program for the measurement of reaction time to visual and auditory stimulus, which was tested on a group of patients and statistically evaluated the reaction time to visual and auditory stimuli. Measurements were performed on the age group from 18 to 28 years, which was not in any way physically or mentally handicapped.
Patient data management in hospital information system Clinicom
Jirásková, Kristýna ; Fedra, Petr (referee) ; Škutková, Helena (advisor)
Hospital information systems to store patient data and to share them. Have several advantages. Doctors are immediately accessible to history, which helps to quickly diagnose, prevent unnecessary wastage of drugs and duplicate tests. The goal of this work was to develop remote access to hospital information system CLINICOM via the Internet. The data in the information system managed by the database system Caché. From this database information was obtained using SQL queries. For the presentation of data on the Internet was designed and implemented user interface in the PHP programming language, which enables remote database management system CLINICOM.
Classification of 1D gel electrophoresis samples
Krupka, Ondřej ; Škutková, Helena (referee) ; Vítek, Martin (advisor)
This term project deals with the classification of 1D gel electrophoresis samples. It describes the theoretical information about gel electrophoresis, various types of errors, processing of the image and its classification using the cluster analysis. One of the main goals is creation of images with the highest quality as possible. A realization of pre-processing and detection of the sample borders is made in the MATLAB environment. And finally, classification of samples is done with subsequent statistical analysis.

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