Efficient repeat finding in sets of strings via suffix arrays

We consider two repeat finding problems relative to sets of strings: (a) Find the largest substrings that occur in every string of a given set; (b) Find the maximal repeats in a given string that occur in no string of a given set. Our solutions are based on the suffix array construction, requiring O...

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Detalles Bibliográficos
Autores: Barenbaum, Pablo, Becher, Veronica Andrea, Deymonnaz, Alejandro, Halsband, Melisa, Heiber, Pablo Ariel
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2013
País:Argentina
Institución:Consejo Nacional de Investigaciones Científicas y Técnicas
Repositorio:CONICET Digital (CONICET)
Idioma:inglés
OAI Identifier:oai:ri.conicet.gov.ar:11336/2502
Acceso en línea:http://hdl.handle.net/11336/2502
Access Level:acceso abierto
Palabra clave:Stringology
Repeats
Suffix Array
Longest Maximal Substring
https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
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spelling Efficient repeat finding in sets of strings via suffix arraysBarenbaum, PabloBecher, Veronica AndreaDeymonnaz, AlejandroHalsband, MelisaHeiber, Pablo ArielStringologyRepeatsSuffix ArrayLongest Maximal Substringhttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1We consider two repeat finding problems relative to sets of strings: (a) Find the largest substrings that occur in every string of a given set; (b) Find the maximal repeats in a given string that occur in no string of a given set. Our solutions are based on the suffix array construction, requiring O(m) memory, where m is the length of the longest input string, and O(n &log;m) time, where n is the the whole input size (the sum of the length of each string in the input). The most expensive part of our algorithms is the computation of several suffix arrays. We give an implementation and experimental results that evidence the efficiency of our algorithms in practice, even for very large inputs.Fil: Barenbaum, Pablo. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Ciudad Universitaria; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; ArgentinaFil: Becher, Veronica Andrea. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; Argentina. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Ciudad Universitaria; ArgentinaFil: Deymonnaz, Alejandro. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; ArgentinaFil: Halsband, Melisa. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; ArgentinaFil: Heiber, Pablo Ariel. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; Argentina. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Ciudad Universitaria; ArgentinaDiscrete Mathematics and Theoretical Computer Science2013-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/2502Barenbaum, Pablo; Becher, Veronica Andrea; Deymonnaz, Alejandro; Halsband, Melisa; Heiber, Pablo Ariel; Efficient repeat finding in sets of strings via suffix arrays; Discrete Mathematics and Theoretical Computer Science; Discrete Mathematics and Theoretical Computer Science; 15; 2; 4-2013; 59-701365-8050enginfo:eu-repo/semantics/altIdentifier/url/https://hal.inria.fr/hal-00980753info:eu-repo/semantics/altIdentifier/url/http://dmtcs.episciences.org/597info:eu-repo/semantics/altIdentifier/url/http://www.dmtcs.org/dmtcs-ojs/index.php/dmtcs/article/view/2130info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2024-05-08T13:53:41Zoai:ri.conicet.gov.ar:11336/2502instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982024-05-08 13:53:41.563CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Efficient repeat finding in sets of strings via suffix arrays
title Efficient repeat finding in sets of strings via suffix arrays
spellingShingle Efficient repeat finding in sets of strings via suffix arrays
Barenbaum, Pablo
Stringology
Repeats
Suffix Array
Longest Maximal Substring
https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
title_short Efficient repeat finding in sets of strings via suffix arrays
title_full Efficient repeat finding in sets of strings via suffix arrays
title_fullStr Efficient repeat finding in sets of strings via suffix arrays
title_full_unstemmed Efficient repeat finding in sets of strings via suffix arrays
title_sort Efficient repeat finding in sets of strings via suffix arrays
dc.creator.none.fl_str_mv Barenbaum, Pablo
Becher, Veronica Andrea
Deymonnaz, Alejandro
Halsband, Melisa
Heiber, Pablo Ariel
author Barenbaum, Pablo
author_facet Barenbaum, Pablo
Becher, Veronica Andrea
Deymonnaz, Alejandro
Halsband, Melisa
Heiber, Pablo Ariel
author_role author
author2 Becher, Veronica Andrea
Deymonnaz, Alejandro
Halsband, Melisa
Heiber, Pablo Ariel
author2_role author
author
author
author
dc.subject.none.fl_str_mv Stringology
Repeats
Suffix Array
Longest Maximal Substring
https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
topic Stringology
Repeats
Suffix Array
Longest Maximal Substring
https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
description We consider two repeat finding problems relative to sets of strings: (a) Find the largest substrings that occur in every string of a given set; (b) Find the maximal repeats in a given string that occur in no string of a given set. Our solutions are based on the suffix array construction, requiring O(m) memory, where m is the length of the longest input string, and O(n &log;m) time, where n is the the whole input size (the sum of the length of each string in the input). The most expensive part of our algorithms is the computation of several suffix arrays. We give an implementation and experimental results that evidence the efficiency of our algorithms in practice, even for very large inputs.
publishDate 2013
dc.date.none.fl_str_mv 2013-04
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/2502
Barenbaum, Pablo; Becher, Veronica Andrea; Deymonnaz, Alejandro; Halsband, Melisa; Heiber, Pablo Ariel; Efficient repeat finding in sets of strings via suffix arrays; Discrete Mathematics and Theoretical Computer Science; Discrete Mathematics and Theoretical Computer Science; 15; 2; 4-2013; 59-70
1365-8050
url http://hdl.handle.net/11336/2502
identifier_str_mv Barenbaum, Pablo; Becher, Veronica Andrea; Deymonnaz, Alejandro; Halsband, Melisa; Heiber, Pablo Ariel; Efficient repeat finding in sets of strings via suffix arrays; Discrete Mathematics and Theoretical Computer Science; Discrete Mathematics and Theoretical Computer Science; 15; 2; 4-2013; 59-70
1365-8050
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://hal.inria.fr/hal-00980753
info:eu-repo/semantics/altIdentifier/url/http://dmtcs.episciences.org/597
info:eu-repo/semantics/altIdentifier/url/http://www.dmtcs.org/dmtcs-ojs/index.php/dmtcs/article/view/2130
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Discrete Mathematics and Theoretical Computer Science
publisher.none.fl_str_mv Discrete Mathematics and Theoretical Computer Science
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1799195476595048448
score 15,812429

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