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Direct Binning of Metagenomic Signals from Nanopore Sequencing
Lebó, Marko ; Jugas, Robin (referee) ; Sedlář, Karel (advisor)
This diploma thesis deals with taxonomy independent methods for classification of metagenomic signals, aquired by a MinION sequencer. It describes the formation and character of metagenomic data and already existing methods of metagenomic data classification and their development. This thesis also evaluates an impact of the third generation sequencing techniques in the world of metagenomics and further specialises on the function of the Oxford Nanopore MinION sequencing device. Lastly, a custom method for metagenomic data classification, based on data obtained from a MinION sequencer, is proposed and compared with an already existing method of classification.
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Application Of Optimization Algorithms To
The Genome Assembly
Jugas, Robin
The paper results from development of new sequencing methods together with the need of suitable genome assembly algorithms. It combines the genomic signal processing, correlation techniques and optimization algorithms for solving assembly task. Genomic signals are made by conversion of letter-based DNA into the form of digital signal, thus the methods of digital signal processing can be applied. Possible overlaps between reads converted into signals are found by computing correlation coefficient similarly to cross-correlation. We acquire similarity matrix and the task is to find the path through it achieving minimum distance criterion. For the task, the two optimization techniques were employed: ant colony optimization (ACO) and simulated annealing (SA). The result implies the possibility of using the ACO at the task of creating path through similarly to graphtheory-based algorithms.
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Evaluation of numerical representations suitability for overlap detection
Pleskačová, Barbora ; Maděránková, Denisa (referee) ; Jugas, Robin (advisor)
The bachelor´s thesis is focused on the evaluation of numerical representations suitability for overlap detection. Introductory part deals with description of deoxyribonucleic acid structure. The next part discribes sequencing methods and genome assembly techniques. Following part deals with numerical representations that convert DNA sequences into numerical form. Based on similarity metrics, the use of these representations is tested for the detection of overlaps between DNA reads. In the practical part of the thesis an algorithm for overlap detection is designed and implemented using numerical representations. The algorithm is then tested on data.
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Homology search using digital signal processing methods
Kamar, Yana ; Jugas, Robin (referee) ; Maděránková, Denisa (advisor)
Thesis includes the theoretical introduction to molecular biology and genetics on the necessary level, including a description of the structure of DNA and the homologous gene. Described are fixed and physic-chemical kinds of nucleotide mapping, methods for processing digital signals. Numerical representations of genes that were programmed in MATLAB: unwrapped and accumulated phases, density vectors. Using the unwrapped phase and density vectors with windows of different lengths was performed CDS searching in the entire genome by calculation metric distances (euclidean and canberian) and correlation. Also, using the metric distances, a homologous gene was found in more or less similar bacterial genomes. The result is the approximate threshold of distance (euclidean and canberian) using to find homologous genes in genome.
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Digital processing of plant genomes
Jugas, Robin ; Škutková, Helena (referee) ; Sedlář, Karel (advisor)
This work continues in development of DNA numerical representation’s field in the recent years. The aim of this bachelor thesis is to work out an overview of numerical representations of DNA sequences and to describe the differences and properties of nuclear and mitochondrial genetic code focused on plants. Final objective is analysis of usability these signal’s representations for classification of organisms. The theoretical part is focused on description of biological facts, overview of conversion methods of DNA sequences into signals, the methods of organisms classification and the DTW algorithm. The practical part contain the created GUI application for organism classification based on numerical sequences and the analysis of usability these numerical representations for classification. The outputs of cluster analysis of numerical sequences are compared with the phylogenetic tree.
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Signal processing based methods for genome assembly refinement
Jugas, Robin ; Provazník, Ivo (referee) ; Sedlář, Karel (advisor)
The diploma thesis deals with sequencing methods and genome assembly methods including usage of numerical representations. The theoretical part of thesis describes the history of DNA research, generations of sequencing methods, the assembly methods themselves and definiton of numerical representations. Numerical represenatations serve to convert character form of DNA to numerical form and so allow to use digital signal processing methods. There is an algorithm for genome assembly using numerical represenatation proposed in thesis, which is later tested at sequence data.
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