License: Creative Commons Attribution 4.0 International license (CC BY 4.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.CPM.2021.22
URN: urn:nbn:de:0030-drops-139736
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2021/13973/
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Park, Sangsoo ; Park, Sung Gwan ; Cazaux, Bastien ; Park, Kunsoo ; Rivals, Eric

A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs

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LIPIcs-CPM-2021-22.pdf (0.9 MB)

Abstract

The hierarchical overlap graph (HOG) is a graph that encodes overlaps from a given set P of n strings, as the overlap graph does. A best known algorithm constructs HOG in O(||P|| log n) time and O(||P||) space, where ||P|| is the sum of lengths of the strings in P. In this paper we present a new algorithm to construct HOG in O(||P||) time and space. Hence, the construction time and space of HOG are better than those of the overlap graph, which are O(||P|| + n²).

BibTeX - Entry

@InProceedings{park_et_al:LIPIcs.CPM.2021.22,
  author =	{Park, Sangsoo and Park, Sung Gwan and Cazaux, Bastien and Park, Kunsoo and Rivals, Eric},
  title =	{{A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs}},
  booktitle =	{32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)},
  pages =	{22:1--22:9},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-186-3},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{191},
  editor =	{Gawrychowski, Pawe{\l} and Starikovskaya, Tatiana},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2021/13973},
  URN =		{urn:nbn:de:0030-drops-139736},
  doi =		{10.4230/LIPIcs.CPM.2021.22},
  annote =	{Keywords: overlap graph, hierarchical overlap graph, shortest superstring problem, border array}
}

Keywords: overlap graph, hierarchical overlap graph, shortest superstring problem, border array
Collection: 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)
Issue Date: 2021
Date of publication: 30.06.2021

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