Digital processing of plant genomes

Práce navazuje na rozvoj v oblasti numerických reprezentací DNA sekvencí v uplynulých letech. Cílem bakalářské práce je zpracovat přehled numerických reprezentací DNA sekvencí a popsat vlastnosti a rozdíly genetického kódu jaderného a mitochondriálního genomu se zaměřením na rostliny. Zakončením je zhodnocení využitelnosti daných signálových reprezentací pro klasifikaci organismů. Teoretická část se zabývá popisem biologických skutečností, přehledem metod konverze DNA sekvence do signálové podoby, metodami klasifikace organismů a algoritmem DTW. Praktická část sestává z vytvoření uživatelské aplikace pro klasifikaci organismů na základě numerických reprezentací a analýza využitelnosti těchto reprezentací pro klasifikaci. Výstupy shlukové analýzy numerických sekvencí jsou srovnány s fylogenetickým stromemThis 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.

Signal processing based methods for genome assembly refinement

Diplomová práce se zabývá sekvenačními metodami a metodami sestavení genomu s využitím numerických reprezentací. Teoretická část práce popisuje historii objevu DNA, jednotlivé generace sekvenačních metod, samotné metody sestavení genomu a definici numerických reprezentací. Numerické reprezentace slouží pro převod znakové podoby DNA do numerické podoby a umožňují tak využití metod digitálního zpracování signálu. V práci je navržen algoritmus pro sestavení genomu s využitím numerické reprezentace, který je dále otestován na datech sekvencí.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.

Application Of Optimization Algorithms To The Genome Assembly

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

Application Of Optimization Algorithms To The Genome Assembly

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