Comparing incomplete sequences via longest common subsequence

Detalhes bibliográficos
Autor(a) principal: Castelli, Mauro
Data de Publicação: 2019
Outros Autores: Dondi, Riccardo, Mauri, Giancarlo, Zoppis, Italo
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: https://doi.org/10.1016/j.tcs.2019.09.022
Resumo: Castelli, M., Dondi, R., Mauri, G., & Zoppis, I. (2019). Comparing incomplete sequences via longest common subsequence. Theoretical Computer Science, 796, 272-285. https://doi.org/10.1016/j.tcs.2019.09.022
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spelling Comparing incomplete sequences via longest common subsequenceApproximation algorithmsComputational complexityFixed-parameter algorithmsLongest common subsequenceString algorithmsTheoretical Computer ScienceComputer Science(all)Castelli, M., Dondi, R., Mauri, G., & Zoppis, I. (2019). Comparing incomplete sequences via longest common subsequence. Theoretical Computer Science, 796, 272-285. https://doi.org/10.1016/j.tcs.2019.09.022Inspired by scaffold filling, a recent approach for genome reconstruction from incomplete data, we consider a variant of the well-known longest common subsequence problem for the comparison of two sequences. The new problem, called Longest Filled Common Subsequence, aims to compare a complete sequence with an incomplete one, i.e. with some missing elements. Longest Filled Common Subsequence (LFCS), given a complete sequence A, an incomplete sequence B, and a multiset M of symbols missing in B, asks for a sequence B⁎ obtained by inserting the symbols of M into B so that B⁎ induces a common subsequence with A of maximum length. We investigate the computational and approximation complexity of the problem and we show that it is NP-hard and APX-hard when A contains at most two occurrences of each symbol, and we give a polynomial time algorithm when the input sequences are over a constant-size alphabet. We give a [Formula presented] approximation algorithm for the Longest Filled Common Subsequence problem. Finally, we present a fixed-parameter algorithm for the problem, when it is parameterized by the number of symbols inserted in B that “match” symbols of A.NOVA Information Management School (NOVA IMS)Information Management Research Center (MagIC) - NOVA Information Management SchoolRUNCastelli, MauroDondi, RiccardoMauri, GiancarloZoppis, Italo2023-03-17T01:31:48Z2019-122019-12-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article14application/pdfhttps://doi.org/10.1016/j.tcs.2019.09.022eng0304-3975PURE: 14929015http://www.scopus.com/inward/record.url?scp=85072570657&partnerID=8YFLogxKhttps://doi.org/10.1016/j.tcs.2019.09.022info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T04:38:36Zoai:run.unl.pt:10362/85834Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:36:38.641196Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Comparing incomplete sequences via longest common subsequence
title Comparing incomplete sequences via longest common subsequence
spellingShingle Comparing incomplete sequences via longest common subsequence
Castelli, Mauro
Approximation algorithms
Computational complexity
Fixed-parameter algorithms
Longest common subsequence
String algorithms
Theoretical Computer Science
Computer Science(all)
title_short Comparing incomplete sequences via longest common subsequence
title_full Comparing incomplete sequences via longest common subsequence
title_fullStr Comparing incomplete sequences via longest common subsequence
title_full_unstemmed Comparing incomplete sequences via longest common subsequence
title_sort Comparing incomplete sequences via longest common subsequence
author Castelli, Mauro
author_facet Castelli, Mauro
Dondi, Riccardo
Mauri, Giancarlo
Zoppis, Italo
author_role author
author2 Dondi, Riccardo
Mauri, Giancarlo
Zoppis, Italo
author2_role author
author
author
dc.contributor.none.fl_str_mv NOVA Information Management School (NOVA IMS)
Information Management Research Center (MagIC) - NOVA Information Management School
RUN
dc.contributor.author.fl_str_mv Castelli, Mauro
Dondi, Riccardo
Mauri, Giancarlo
Zoppis, Italo
dc.subject.por.fl_str_mv Approximation algorithms
Computational complexity
Fixed-parameter algorithms
Longest common subsequence
String algorithms
Theoretical Computer Science
Computer Science(all)
topic Approximation algorithms
Computational complexity
Fixed-parameter algorithms
Longest common subsequence
String algorithms
Theoretical Computer Science
Computer Science(all)
description Castelli, M., Dondi, R., Mauri, G., & Zoppis, I. (2019). Comparing incomplete sequences via longest common subsequence. Theoretical Computer Science, 796, 272-285. https://doi.org/10.1016/j.tcs.2019.09.022
publishDate 2019
dc.date.none.fl_str_mv 2019-12
2019-12-01T00:00:00Z
2023-03-17T01:31:48Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv https://doi.org/10.1016/j.tcs.2019.09.022
url https://doi.org/10.1016/j.tcs.2019.09.022
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 0304-3975
PURE: 14929015
http://www.scopus.com/inward/record.url?scp=85072570657&partnerID=8YFLogxK
https://doi.org/10.1016/j.tcs.2019.09.022
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 14
application/pdf
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
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instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
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reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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