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Article: Structural alignment of RNA with complex pseudoknot structure

TitleStructural alignment of RNA with complex pseudoknot structure
Authors
Keywordsdynamic programming
secondary structure
sequences
Issue Date2011
PublisherMary Ann Liebert, Inc Publishers. The Journal's web site is located at http://www.liebertpub.com/cmb
Citation
Journal Of Computational Biology, 2011, v. 18 n. 1, p. 97-108 How to Cite?
Abstract
The secondary structure of an ncRNA molecule is known to play an important role in its biological functions. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, existing algorithms cannot handle complex pseudoknot structures which are found in nature. In this article, we propose algorithms to handle two types of complex pseudoknots: simple non-standard pseudoknots and recursive pseudoknots. Although our methods are not designed for general pseudoknots, it already covers all known ncRNAs in both Rfam and PseudoBase databases. An evaluation of our algorithms shows that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA. © Copyright 2011, Mary Ann Liebert, Inc.
Persistent Identifierhttp://hdl.handle.net/10722/140797
ISSN
2013 Impact Factor: 1.670
2013 SCImago Journal Rankings: 1.367
ISI Accession Number ID
References

 

Author Affiliations
  1. The University of Hong Kong
  2. National University of Singapore
DC FieldValueLanguage
dc.contributor.authorWong, TKFen_HK
dc.contributor.authorLam, TWen_HK
dc.contributor.authorSung, WKen_HK
dc.contributor.authorCheung, BWYen_HK
dc.contributor.authorYiu, SMen_HK
dc.date.accessioned2011-09-23T06:19:29Z-
dc.date.available2011-09-23T06:19:29Z-
dc.date.issued2011en_HK
dc.identifier.citationJournal Of Computational Biology, 2011, v. 18 n. 1, p. 97-108en_HK
dc.identifier.issn1066-5277en_HK
dc.identifier.urihttp://hdl.handle.net/10722/140797-
dc.description.abstractThe secondary structure of an ncRNA molecule is known to play an important role in its biological functions. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, existing algorithms cannot handle complex pseudoknot structures which are found in nature. In this article, we propose algorithms to handle two types of complex pseudoknots: simple non-standard pseudoknots and recursive pseudoknots. Although our methods are not designed for general pseudoknots, it already covers all known ncRNAs in both Rfam and PseudoBase databases. An evaluation of our algorithms shows that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA. © Copyright 2011, Mary Ann Liebert, Inc.en_HK
dc.languageengen_US
dc.publisherMary Ann Liebert, Inc Publishers. The Journal's web site is located at http://www.liebertpub.com/cmben_HK
dc.relation.ispartofJournal of Computational Biologyen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subjectdynamic programmingen_HK
dc.subjectsecondary structureen_HK
dc.subjectsequencesen_HK
dc.subject.meshComputer Simulation-
dc.subject.meshModels, Molecular-
dc.subject.meshMolecular Sequence Data-
dc.subject.meshNucleic Acid Conformation-
dc.subject.meshRNA, Untranslated - chemistry - classification-
dc.titleStructural alignment of RNA with complex pseudoknot structureen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1066-5277&volume=18&issue=1&spage=97&epage=108&date=2011&atitle=Structural+alignment+of+RNA+with+complex+pseudoknot+structure-
dc.identifier.emailLam, TW:twlam@cs.hku.hken_HK
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_HK
dc.identifier.authorityLam, TW=rp00135en_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.description.naturepublished_or_final_versionen_US
dc.identifier.doi10.1089/cmb.2009.0275en_HK
dc.identifier.pmid21210732en_HK
dc.identifier.scopuseid_2-s2.0-78651323987en_HK
dc.identifier.hkuros192237en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-78651323987&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume18en_HK
dc.identifier.issue1en_HK
dc.identifier.spage97en_HK
dc.identifier.epage108en_HK
dc.identifier.isiWOS:000285965600008-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridWong, TKF=25423289800en_HK
dc.identifier.scopusauthoridLam, TW=7202523165en_HK
dc.identifier.scopusauthoridSung, WK=13310059700en_HK
dc.identifier.scopusauthoridCheung, BWY=36132876900en_HK
dc.identifier.scopusauthoridYiu, SM=7003282240en_HK
dc.identifier.citeulike9456142-

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