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Article: Efficient constrained multiple sequence alignment with performance guarantee.

TitleEfficient constrained multiple sequence alignment with performance guarantee.
Authors
Issue Date2003
Citation
Proceedings / Ieee Computer Society Bioinformatics Conference. Ieee Computer Society Bioinformatics Conference., 2003, v. 2, p. 337-346 How to Cite?
AbstractThe Constrained Multiple Sequence Alignment problem is to align a set of sequences 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 [14], 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(n(4))-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.
Persistent Identifierhttp://hdl.handle.net/10722/152319
ISSN

 

DC FieldValueLanguage
dc.contributor.authorChin, FYen_US
dc.contributor.authorHo, NLen_US
dc.contributor.authorLam, TWen_US
dc.contributor.authorWong, PWen_US
dc.contributor.authorChan, MYen_US
dc.date.accessioned2012-06-26T06:37:10Z-
dc.date.available2012-06-26T06:37:10Z-
dc.date.issued2003en_US
dc.identifier.citationProceedings / Ieee Computer Society Bioinformatics Conference. Ieee Computer Society Bioinformatics Conference., 2003, v. 2, p. 337-346en_US
dc.identifier.issn1555-3930en_US
dc.identifier.urihttp://hdl.handle.net/10722/152319-
dc.description.abstractThe Constrained Multiple Sequence Alignment problem is to align a set of sequences 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 [14], 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(n(4))-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.en_US
dc.languageengen_US
dc.relation.ispartofProceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference.en_US
dc.subject.meshAlgorithmsen_US
dc.subject.meshAmino Acid Sequenceen_US
dc.subject.meshBase Sequenceen_US
dc.subject.meshMolecular Sequence Dataen_US
dc.subject.meshPattern Recognition, Automated - Methodsen_US
dc.subject.meshSequence Alignment - Methodsen_US
dc.subject.meshSequence Analysis - Methodsen_US
dc.subject.meshSoftwareen_US
dc.titleEfficient constrained multiple sequence alignment with performance guarantee.en_US
dc.typeArticleen_US
dc.identifier.emailChin, FY:chin@cs.hku.hken_US
dc.identifier.emailLam, TW:twlam@cs.hku.hken_US
dc.identifier.authorityChin, FY=rp00105en_US
dc.identifier.authorityLam, TW=rp00135en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.pmid16452809-
dc.identifier.scopuseid_2-s2.0-1842799018en_US
dc.identifier.volume2en_US
dc.identifier.spage337en_US
dc.identifier.epage346en_US
dc.identifier.scopusauthoridChin, FY=7005101915en_US
dc.identifier.scopusauthoridHo, NL=7102776259en_US
dc.identifier.scopusauthoridLam, TW=7202523165en_US
dc.identifier.scopusauthoridWong, PW=9734871500en_US
dc.identifier.scopusauthoridChan, MY=7402597863en_US

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