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Article: Efficient constrained multiple sequence alignment with performance guarantee

TitleEfficient constrained multiple sequence alignment with performance guarantee
Authors
Issue Date2005
PublisherImperial College Press. The Journal's web site is located at http://www.worldscinet.com/jbcb/jbcb.shtml
Citation
Journal Of Bioinformatics And Computational Biology, 2005, v. 3 n. 1, p. 1-18 How to Cite?
AbstractThe constrained multiple sequence alignment problem is to align a set of sequences of maximum length n subject to a given constrained sequence, which arises from some knowledge of the structure of the sequences. This paper presents new algorithms for this problem, which are more efficient in terms of time and space (memory) than the previous algorithms,15 and with a worst-case guarantee on the quality of the alignment. Saving the space requirement by a quadratic factor is particularly significant as the previous O(n4)-space algorithm has limited application due to its huge memory requirement. Experiments on real data sets confirm that our new algorithms show improvements in both alignment quality and resource requirements. © Imperial College Press.
Persistent Identifierhttp://hdl.handle.net/10722/152317
ISSN
2015 Impact Factor: 0.785
2015 SCImago Journal Rankings: 0.525
References

 

DC FieldValueLanguage
dc.contributor.authorChin, FYLen_US
dc.contributor.authorHo, NLen_US
dc.contributor.authorLam, TWen_US
dc.contributor.authorWong, PWHen_US
dc.date.accessioned2012-06-26T06:37:08Z-
dc.date.available2012-06-26T06:37:08Z-
dc.date.issued2005en_US
dc.identifier.citationJournal Of Bioinformatics And Computational Biology, 2005, v. 3 n. 1, p. 1-18en_US
dc.identifier.issn0219-7200en_US
dc.identifier.urihttp://hdl.handle.net/10722/152317-
dc.description.abstractThe constrained multiple sequence alignment problem is to align a set of sequences of maximum length n subject to a given constrained sequence, which arises from some knowledge of the structure of the sequences. This paper presents new algorithms for this problem, which are more efficient in terms of time and space (memory) than the previous algorithms,15 and with a worst-case guarantee on the quality of the alignment. Saving the space requirement by a quadratic factor is particularly significant as the previous O(n4)-space algorithm has limited application due to its huge memory requirement. Experiments on real data sets confirm that our new algorithms show improvements in both alignment quality and resource requirements. © Imperial College Press.en_US
dc.languageengen_US
dc.publisherImperial College Press. The Journal's web site is located at http://www.worldscinet.com/jbcb/jbcb.shtmlen_US
dc.relation.ispartofJournal of Bioinformatics and Computational Biologyen_US
dc.subject.meshAlgorithmsen_US
dc.subject.meshConserved Sequenceen_US
dc.subject.meshRibonucleases - Analysis - Chemistryen_US
dc.subject.meshSequence Alignment - Methodsen_US
dc.subject.meshSequence Analysis - Methodsen_US
dc.subject.meshSequence Homologyen_US
dc.titleEfficient constrained multiple sequence alignment with performance guaranteeen_US
dc.typeArticleen_US
dc.identifier.emailChin, FYL:chin@cs.hku.hken_US
dc.identifier.emailLam, TW:twlam@cs.hku.hken_US
dc.identifier.authorityChin, FYL=rp00105en_US
dc.identifier.authorityLam, TW=rp00135en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1142/S0219720005000977en_US
dc.identifier.pmid15751109-
dc.identifier.scopuseid_2-s2.0-14544306213en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-14544306213&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume3en_US
dc.identifier.issue1en_US
dc.identifier.spage1en_US
dc.identifier.epage18en_US
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridChin, FYL=7005101915en_US
dc.identifier.scopusauthoridHo, NL=7102776259en_US
dc.identifier.scopusauthoridLam, TW=7202523165en_US
dc.identifier.scopusauthoridWong, PWH=9734871500en_US

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