Show simple item record

Efektivní reprezentace množin k-merů
dc.contributor.advisorVeselý, Pavel
dc.creatorMilyutina, Ekaterina
dc.date.accessioned2023-11-07T01:16:12Z
dc.date.available2023-11-07T01:16:12Z
dc.date.issued2023
dc.identifier.urihttp://hdl.handle.net/20.500.11956/184307
dc.description.abstractIn 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.languageEnglishcs_CZ
dc.language.isoen_US
dc.publisherUniverzita Karlova, Matematicko-fyzikální fakultacs_CZ
dc.subjectmnožiny k-merů|nejkratší nadřetězec|bioinformatika|hladový algoritmuscs_CZ
dc.subjectk-mer sets|shortest superstring|bioinformatics|greedy algorithmen_US
dc.titleEfficient representation of k-mer setsen_US
dc.typebakalářská prácecs_CZ
dcterms.created2023
dcterms.dateAccepted2023-09-07
dc.description.departmentInformatický ústav Univerzity Karlovycs_CZ
dc.description.departmentComputer Science Institute of Charles Universityen_US
dc.description.facultyMatematicko-fyzikální fakultacs_CZ
dc.description.facultyFaculty of Mathematics and Physicsen_US
dc.identifier.repId249202
dc.title.translatedEfektivní reprezentace množin k-merůcs_CZ
dc.contributor.refereeKolman, Petr
thesis.degree.nameBc.
thesis.degree.levelbakalářskécs_CZ
thesis.degree.disciplineObecná informatikacs_CZ
thesis.degree.disciplineGeneral Computer Scienceen_US
thesis.degree.programInformatikacs_CZ
thesis.degree.programComputer Scienceen_US
uk.thesis.typebakalářská prácecs_CZ
uk.taxonomy.organization-csMatematicko-fyzikální fakulta::Informatický ústav Univerzity Karlovycs_CZ
uk.taxonomy.organization-enFaculty of Mathematics and Physics::Computer Science Institute of Charles Universityen_US
uk.faculty-name.csMatematicko-fyzikální fakultacs_CZ
uk.faculty-name.enFaculty of Mathematics and Physicsen_US
uk.faculty-abbr.csMFFcs_CZ
uk.degree-discipline.csObecná informatikacs_CZ
uk.degree-discipline.enGeneral Computer Scienceen_US
uk.degree-program.csInformatikacs_CZ
uk.degree-program.enComputer Scienceen_US
thesis.grade.csDobřecs_CZ
thesis.grade.enGooden_US
uk.abstract.enIn 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-availabilityV
uk.grantorUniverzita Karlova, Matematicko-fyzikální fakulta, Informatický ústav Univerzity Karlovycs_CZ
thesis.grade.code3
dc.contributor.consultantBřinda, Karel
uk.publication-placePrahacs_CZ
uk.thesis.defenceStatusO


Files in this item

Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail

This item appears in the following Collection(s)

Show simple item record


© 2017 Univerzita Karlova, Ústřední knihovna, Ovocný trh 560/5, 116 36 Praha 1; email: admin-repozitar [at] cuni.cz

Za dodržení všech ustanovení autorského zákona jsou zodpovědné jednotlivé složky Univerzity Karlovy. / Each constituent part of Charles University is responsible for adherence to all provisions of the copyright law.

Upozornění / Notice: Získané informace nemohou být použity k výdělečným účelům nebo vydávány za studijní, vědeckou nebo jinou tvůrčí činnost jiné osoby než autora. / Any retrieved information shall not be used for any commercial purposes or claimed as results of studying, scientific or any other creative activities of any person other than the author.

DSpace software copyright © 2002-2015  DuraSpace
Theme by 
@mire NV