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Conference Paper: Improved approximate string matching using compressed suffix data structures

TitleImproved approximate string matching using compressed suffix data structures
Authors
Issue Date2008
PublisherSpringer New York LLC. The Journal's web site is located at http://link.springer.de/link/service/journals/00453/index.htm
Citation
Algorithmica (New York), 2008, v. 51 n. 3, p. 298-314 How to Cite?
AbstractApproximate string matching is about finding a given string pattern in a text by allowing some degree of errors. In this paper we present a space efficient data structure to solve the 1-mismatch and 1-difference problems. Given a text T of length n over an alphabet A, we can preprocess T and give an O(n √log n log |A|)-bit space data structure so that, for any query pattern P of length m, we can find all 1-mismatch (or 1-difference) occurrences of P in O(|A|m log log n+occ) time, where occ is the number of occurrences. This is the fastest known query time given that the space of the data structure is o(n log2 n) bits. The space of our data structure can be further reduced to O(n log |A|) with the query time increasing by a factor of log ε n, for 0 < ε ≤ 1. Furthermore, our solution can be generalized to solve the k-mismatch (and the k-difference) problem in O(|A| k mk (k + log log n) + occ) and O(logε n(|A|k mk (k + log log n) + occ)) time using an O(n √log n log |A|)-bit and an O(n log |A|)-bit indexing data structures, respectively. We assume that the alphabet size |A| is bounded by O(2 √log n) for the O(n√log n log |A|)-bit space data structure. © 2007 Springer Science+Business Media, LLC.
Persistent Identifierhttp://hdl.handle.net/10722/151910
ISSN
2014 Impact Factor: 0.791
2014 SCImago Journal Rankings: 1.433
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorLam, TWen_US
dc.contributor.authorSung, WKen_US
dc.contributor.authorWong, SSen_US
dc.date.accessioned2012-06-26T06:30:42Z-
dc.date.available2012-06-26T06:30:42Z-
dc.date.issued2008en_US
dc.identifier.citationAlgorithmica (New York), 2008, v. 51 n. 3, p. 298-314en_US
dc.identifier.issn0178-4617en_US
dc.identifier.urihttp://hdl.handle.net/10722/151910-
dc.description.abstractApproximate string matching is about finding a given string pattern in a text by allowing some degree of errors. In this paper we present a space efficient data structure to solve the 1-mismatch and 1-difference problems. Given a text T of length n over an alphabet A, we can preprocess T and give an O(n √log n log |A|)-bit space data structure so that, for any query pattern P of length m, we can find all 1-mismatch (or 1-difference) occurrences of P in O(|A|m log log n+occ) time, where occ is the number of occurrences. This is the fastest known query time given that the space of the data structure is o(n log2 n) bits. The space of our data structure can be further reduced to O(n log |A|) with the query time increasing by a factor of log ε n, for 0 < ε ≤ 1. Furthermore, our solution can be generalized to solve the k-mismatch (and the k-difference) problem in O(|A| k mk (k + log log n) + occ) and O(logε n(|A|k mk (k + log log n) + occ)) time using an O(n √log n log |A|)-bit and an O(n log |A|)-bit indexing data structures, respectively. We assume that the alphabet size |A| is bounded by O(2 √log n) for the O(n√log n log |A|)-bit space data structure. © 2007 Springer Science+Business Media, LLC.en_US
dc.languageengen_US
dc.publisherSpringer New York LLC. The Journal's web site is located at http://link.springer.de/link/service/journals/00453/index.htmen_US
dc.relation.ispartofAlgorithmica (New York)en_US
dc.titleImproved approximate string matching using compressed suffix data structuresen_US
dc.typeConference_Paperen_US
dc.identifier.emailLam, TW:twlam@cs.hku.hken_US
dc.identifier.authorityLam, TW=rp00135en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1007/s00453-007-9104-8en_US
dc.identifier.scopuseid_2-s2.0-43949112336en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-43949112336&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume51en_US
dc.identifier.issue3en_US
dc.identifier.spage298en_US
dc.identifier.epage314en_US
dc.identifier.isiWOS:000255874200005-
dc.publisher.placeUnited Statesen_US
dc.identifier.scopusauthoridLam, TW=7202523165en_US
dc.identifier.scopusauthoridSung, WK=13310059700en_US
dc.identifier.scopusauthoridWong, SS=8439889300en_US

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