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Numerical representations of protein sequences for classification
Bartoň, Vojtěch ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
Todays we have the opportunity to analyze huge sets of genomics and proteomics data. In my bachaleor thesis I introduce a few numerical alternatives to represent proteins. The usage of numerical representations opened the way to analyze proteomics data as digital signals, which bring us quantity of new possibilities how to process the protein. In my thesis I compare a few numerical representation with standard taxonomy and with symbolic representation too.
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Methods for gene prediction in prokaryotic genomes
Nykrýnová, Markéta ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis deals with methods of gene prediction in prokaryotic genomes. First part of the thesis introduces prokaryotic cell, its genome, expression of genetic information and methods for gene prediction. Following part describes three software products for gene prediction. Chosen software was tested against specific genome and next chapter presents obtained results. The last part describes program called Gene_finder and its results.
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Methods of DNA tandem repeats analysis
Havlík, Kryštof ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
This work clarifies basics of the repetitive DNA and evaluates thee tandem repeats finders, which are accessible to public free of payment. Second part describes an algorithm used for searching tandem repeats, based on converting DNA string into numerical signal. Then follows signal processing using short-time Fourier transform, formation of spectrogram and analysis for evaluating position and content of repetitive areas. Result of this work is comparison of outcomes provided by public accessible programs with results of created program and review of advantages and disadvantages.
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User interface for data extraction from GenBank data format
Jurečková, Kateřina ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis contains a literature review on the topic of the GenBank database, its most used flat file format gbk and its comparison with other formats of sequential data. Furthermore this thesis describes the structure of mitochondrial DNA of animals and plants and plastid DNA of plants. In the practical part of this thesis is evaluation of successful automatic data extraction from GenBank flat file format from whole mitochondrial sequences by genbankread function in Matlab. And it describes also a new application for GenBank data extraction. In the end this application is used in analyses of mitochondrial genomes.
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Transcription motif finding algorithms
Peřinová, Barbora ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis deals with finding transcription motifs in DNA sequences. The first part describes the DNA transcription process, the significance of transcription motifs and provides an overview of transcription motif databases. The second part contains the classification of transcription motif finding algorithms, and details seven existing algorithms. In the practical part, functions for the analysis according to the Oligo-Analysis algorithm were created. Created functions were validated on the artificially created sequences with introduced motifs. The analysis of two families of coregulated genes was realized and the results were compared with the values achieved by the authors of the Oligo-Analysis algorithm.
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Evolutionary models for evaluation of organisms relationship
Gregorová, Kateřina ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The work is focused on the study and description of evolutionary models for the evaluation of the evolutionary distances of DNA sequences and protein sequences in the amino acids and the codon representation. In the framework of this work was created a program that evaluates the genetic distance between DNA sequences and protein sequences for the use of some evolutionary models. The program calculates the genetic distance of the compared sequences and on the basis thereof renders the phylogenetic tree. This can be relatively easily and quickly evaluate the affinity of the organisms. For easy operation is part of the evaluation program also graphical user interface (GUI).
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Comparison of genomes by synteny block analysis
Pavel, Tomáš ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
The theoretical part of this bachelor thesis is aimed at basics of genetics. Term of gene and mutation are introduced in this section. There are gene and chromosome mutations mentioned and described. Following section is devoted to comparative genomics and especially to synteny. There is described what the synteny actually is and how the synteny arises. The end of the theoretical part of this thesis is about the evolution and there are described ways of sorting permutation vectors. The practical part of this bachelor thesis includes description of developed software. Output of this software is a dot-plot which shows detected synteny blocks. Indexes of these blocks are listed in GUI. The second important output is number of permutation steps. This number determines evolutionary distance between two analysed DNA sequences. The very last section is aimed at analyse of synthetic and real DNA sequences.
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Effect of different numerical representations of DNA on molecular taxonomy
Blaschová, Eliška ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
This paper introduces the classical and molecular taxonomy used for classification of organisms. It represents the direction of DNA barcoding as a possibility to identify unknown organism. Acquired mitochondrial DNA sequences in DNA barcoding can by transform by suitable method to numerical representation that will properly inform about the organisms relationship to other taxa. In this work, we consider three methods of numerical representation: the 1st and 4th quadrant EIIP values and 3D numerical representation reduction. The practical part is programmed identification analysis, which assigns the test organisms reference organism. Testing is performed at 4 reference files and analyzed 5 files. The work summarized the success assigning the correct reference for the selected method of numerical representation.
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