| Meno: | Eva
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| Priezvisko: | Herencsárová
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| Názov: | Identifying Clusters in Graph Representations of Genomes
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| Vedúci: | doc. Mgr. Bronislava Brejová, PhD.
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| Rok: | 2023
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| Kµúčové slová: | pan-genome, elastic-degenerate string, maximum-sum segments problem, path-decomposition, path-width
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| Abstrakt: | In many bioinformatics applications, we identify biologically significant locations
in an individual genome. These locations may represent for example mutations,
genes or positions with a particular biological role. In our work, we are interested
in finding clusters with high density of such biologically meaningful locations
in a graphical pan-genome, which is a collection of related genomes represented
by a graph. Vertices in these graphs correspond to parts of the sequences and
edges to adjacencies between them. In this work we study existing methods for
finding such dense clusters in linear sequences, and extend them to graphs. We
implemented one of our algorithms and used it to search for GC-rich regions in
an elastic-degenerate string, which is a specific representation of a pan-genome.
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