Article: A space and time efficient algorithm for constructing compressed suffix arrays

File Download Links for fulltext
(May Require Subscription)
Supplementary
  • Basic View
  • Metadata View
  • XML View
TitleA space and time efficient algorithm for constructing compressed suffix arrays
AuthorsHon, WK2
Lam, TW2
Sadakane, K1
Sung, WK3
Yiu, SM2
KeywordsCompression
Construcion
Pattern mathching
Text indexing
Issue Date2007
PublisherSpringer New York LLC. The Journal's web site is located at http://link.springer.de/link/service/journals/00453/index.htm
CitationAlgorithmica (New York), 2007, v. 48 n. 1, p. 23-36 [How to Cite?]
DOI: http://dx.doi.org/10.1007/s00453-006-1228-8
AbstractWith the first human DNA being decoded into a sequence of about 2.8 billion characters, much biological research has been centered on analyzing this sequence. Theoretically speaking, it is now feasible to accommodate an index for human DNA in the main memory so that any pattern can be located efficiently. This is due to the recent breakthrough on compressed suffix arrays, which reduces the space requirement from O(n log n) bits to O(n) bits. However, constructing compressed suffix arrays is still not an easy task because we still have to compute suffix arrays first and need a working memory of O(n log n) bits (i.e., more than 13 gigabytes for human DNA). This paper initiates the study of constructing compressed suffix arrays directly from the text. The main contribution is a construction algorithm that uses only O(n) bits of working memory, and the time complexity is O(n log n). Our construction algorithm is also time and space efficient for texts with large alphabets such as Chinese or Japanese. Precisely, when the alphabet size is |∑|, the working space is O(n log |∑|) bits, and the time complexity remains O(n log n), which is independent of |∑|. © Springer 2007.
ISSN0178-4617
2011 Impact Factor: 0.604
2011 SCImago Journal Rankings: 0.042
DOIhttp://dx.doi.org/10.1007/s00453-006-1228-8
ISI Accession Number IDWOS:000246152800002
ReferencesReferences in Scopus
DC Field
Value
dc.contributor.authorHon, WK
dc.contributor.authorLam, TW
dc.contributor.authorSadakane, K
dc.contributor.authorSung, WK
dc.contributor.authorYiu, SM
dc.date.accessioned2010-09-06T09:50:31Z
dc.date.available2010-09-06T09:50:31Z
dc.date.issued2007
dc.description.abstractWith the first human DNA being decoded into a sequence of about 2.8 billion characters, much biological research has been centered on analyzing this sequence. Theoretically speaking, it is now feasible to accommodate an index for human DNA in the main memory so that any pattern can be located efficiently. This is due to the recent breakthrough on compressed suffix arrays, which reduces the space requirement from O(n log n) bits to O(n) bits. However, constructing compressed suffix arrays is still not an easy task because we still have to compute suffix arrays first and need a working memory of O(n log n) bits (i.e., more than 13 gigabytes for human DNA). This paper initiates the study of constructing compressed suffix arrays directly from the text. The main contribution is a construction algorithm that uses only O(n) bits of working memory, and the time complexity is O(n log n). Our construction algorithm is also time and space efficient for texts with large alphabets such as Chinese or Japanese. Precisely, when the alphabet size is |∑|, the working space is O(n log |∑|) bits, and the time complexity remains O(n log n), which is independent of |∑|. © Springer 2007.
dc.description.natureLink_to_subscribed_fulltext
dc.identifier.citationAlgorithmica (New York), 2007, v. 48 n. 1, p. 23-36 [How to Cite?]
DOI: http://dx.doi.org/10.1007/s00453-006-1228-8
dc.identifier.citeulike4736346
dc.identifier.doihttp://dx.doi.org/10.1007/s00453-006-1228-8
dc.identifier.epage36
dc.identifier.hkuros128171
dc.identifier.isiWOS:000246152800002
dc.identifier.issn0178-4617
2011 Impact Factor: 0.604
2011 SCImago Journal Rankings: 0.042
dc.identifier.issue1
dc.identifier.openurl
dc.identifier.scopuseid_2-s2.0-34547375123
dc.identifier.spage23
dc.identifier.urihttp://hdl.handle.net/10722/88951
dc.identifier.volume48
dc.languageeng
dc.publisherSpringer New York LLC. The Journal's web site is located at http://link.springer.de/link/service/journals/00453/index.htm
dc.publisher.placeUnited States
dc.relation.ispartofAlgorithmica (New York)
dc.relation.referencesReferences in Scopus
dc.subjectCompression
dc.subjectConstrucion
dc.subjectPattern mathching
dc.subjectText indexing
dc.titleA space and time efficient algorithm for constructing compressed suffix arrays
dc.typeArticle
Author Affiliations
  1. Kyushu University
  2. The University of Hong Kong
  3. National University of Singapore