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/
Park, Sangsoo ;
Park, Sung Gwan ;
Cazaux, Bastien ;
Park, Kunsoo ;
Rivals, Eric
A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs
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: |
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overlap graph, hierarchical overlap graph, shortest superstring problem, border array |
Collection: |
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32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021) |
Issue Date: |
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2021 |
Date of publication: |
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30.06.2021 |