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Article: Structural alignment of RNA with complex pseudoknot structure
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TitleStructural alignment of RNA with complex pseudoknot structure
 
AuthorsWong, TKF1
Lam, TW1
Sung, WK2
Cheung, BWY1
Yiu, SM1
 
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
 
CitationJournal Of Computational Biology, 2011, v. 18 n. 1, p. 97-108 [How to Cite?]
DOI: http://dx.doi.org/10.1089/cmb.2009.0275
 
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.
 
ISSN1066-5277
2012 Impact Factor: 1.564
2012 SCImago Journal Rankings: 1.056
 
DOIhttp://dx.doi.org/10.1089/cmb.2009.0275
 
ISI Accession Number IDWOS:000285965600008
 
ReferencesReferences in Scopus
 
DC FieldValue
dc.contributor.authorWong, TKF
 
dc.contributor.authorLam, TW
 
dc.contributor.authorSung, WK
 
dc.contributor.authorCheung, BWY
 
dc.contributor.authorYiu, SM
 
dc.date.accessioned2011-09-23T06:19:29Z
 
dc.date.available2011-09-23T06:19:29Z
 
dc.date.issued2011
 
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.
 
dc.description.naturepublished_or_final_version
 
dc.identifier.citationJournal Of Computational Biology, 2011, v. 18 n. 1, p. 97-108 [How to Cite?]
DOI: http://dx.doi.org/10.1089/cmb.2009.0275
 
dc.identifier.citeulike9456142
 
dc.identifier.doihttp://dx.doi.org/10.1089/cmb.2009.0275
 
dc.identifier.epage108
 
dc.identifier.hkuros192237
 
dc.identifier.isiWOS:000285965600008
 
dc.identifier.issn1066-5277
2012 Impact Factor: 1.564
2012 SCImago Journal Rankings: 1.056
 
dc.identifier.issue1
 
dc.identifier.openurl
 
dc.identifier.pmid21210732
 
dc.identifier.scopuseid_2-s2.0-78651323987
 
dc.identifier.spage97
 
dc.identifier.urihttp://hdl.handle.net/10722/140797
 
dc.identifier.volume18
 
dc.languageeng
 
dc.publisherMary Ann Liebert, Inc Publishers. The Journal's web site is located at http://www.liebertpub.com/cmb
 
dc.publisher.placeUnited States
 
dc.relation.ispartofJournal of Computational Biology
 
dc.relation.referencesReferences in Scopus
 
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License
 
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.subjectdynamic programming
 
dc.subjectsecondary structure
 
dc.subjectsequences
 
dc.titleStructural alignment of RNA with complex pseudoknot structure
 
dc.typeArticle
 
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Author Affiliations
  1. The University of Hong Kong
  2. National University of Singapore