dc.contributor.advisor | Veselý, Pavel | |
dc.creator | Milyutina, Ekaterina | |
dc.date.accessioned | 2023-11-07T01:16:12Z | |
dc.date.available | 2023-11-07T01:16:12Z | |
dc.date.issued | 2023 | |
dc.identifier.uri | http://hdl.handle.net/20.500.11956/184307 | |
dc.description.abstract | In this thesis we explore and compare various methods for efficient k-mer set representation. We evaluate traditional de Bruijn graph representation techniques against greedy approximation algorithms for the Shortest Superstring Problem. We describe the linear- time implementation of the well-known Greedy algorithm by Ukkonen [1990] and extend it to another related algorithm, called TGreedy. In addition, we test selected algorithms on a bacterial genome and pangenome to highlight the differences in the size of their output representation and the computational resources used, providing an insight into their respective efficiencies. | en_US |
dc.language | English | cs_CZ |
dc.language.iso | en_US | |
dc.publisher | Univerzita Karlova, Matematicko-fyzikální fakulta | cs_CZ |
dc.subject | množiny k-merů|nejkratší nadřetězec|bioinformatika|hladový algoritmus | cs_CZ |
dc.subject | k-mer sets|shortest superstring|bioinformatics|greedy algorithm | en_US |
dc.title | Efficient representation of k-mer sets | en_US |
dc.type | bakalářská práce | cs_CZ |
dcterms.created | 2023 | |
dcterms.dateAccepted | 2023-09-07 | |
dc.description.department | Informatický ústav Univerzity Karlovy | cs_CZ |
dc.description.department | Computer Science Institute of Charles University | en_US |
dc.description.faculty | Matematicko-fyzikální fakulta | cs_CZ |
dc.description.faculty | Faculty of Mathematics and Physics | en_US |
dc.identifier.repId | 249202 | |
dc.title.translated | Efektivní reprezentace množin k-merů | cs_CZ |
dc.contributor.referee | Kolman, Petr | |
thesis.degree.name | Bc. | |
thesis.degree.level | bakalářské | cs_CZ |
thesis.degree.discipline | Obecná informatika | cs_CZ |
thesis.degree.discipline | General Computer Science | en_US |
thesis.degree.program | Informatika | cs_CZ |
thesis.degree.program | Computer Science | en_US |
uk.thesis.type | bakalářská práce | cs_CZ |
uk.taxonomy.organization-cs | Matematicko-fyzikální fakulta::Informatický ústav Univerzity Karlovy | cs_CZ |
uk.taxonomy.organization-en | Faculty of Mathematics and Physics::Computer Science Institute of Charles University | en_US |
uk.faculty-name.cs | Matematicko-fyzikální fakulta | cs_CZ |
uk.faculty-name.en | Faculty of Mathematics and Physics | en_US |
uk.faculty-abbr.cs | MFF | cs_CZ |
uk.degree-discipline.cs | Obecná informatika | cs_CZ |
uk.degree-discipline.en | General Computer Science | en_US |
uk.degree-program.cs | Informatika | cs_CZ |
uk.degree-program.en | Computer Science | en_US |
thesis.grade.cs | Dobře | cs_CZ |
thesis.grade.en | Good | en_US |
uk.abstract.en | In this thesis we explore and compare various methods for efficient k-mer set representation. We evaluate traditional de Bruijn graph representation techniques against greedy approximation algorithms for the Shortest Superstring Problem. We describe the linear- time implementation of the well-known Greedy algorithm by Ukkonen [1990] and extend it to another related algorithm, called TGreedy. In addition, we test selected algorithms on a bacterial genome and pangenome to highlight the differences in the size of their output representation and the computational resources used, providing an insight into their respective efficiencies. | en_US |
uk.file-availability | V | |
uk.grantor | Univerzita Karlova, Matematicko-fyzikální fakulta, Informatický ústav Univerzity Karlovy | cs_CZ |
thesis.grade.code | 3 | |
dc.contributor.consultant | Břinda, Karel | |
uk.publication-place | Praha | cs_CZ |
uk.thesis.defenceStatus | O | |