Article: Structural alignment of RNA with complex pseudoknot structure

File Download Links for fulltext
(May Require Subscription)
Supplementary
  • Basic View
  • Metadata View
  • XML View
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
2011 Impact Factor: 1.546
2011 SCImago Journal Rankings: 0.263
DOIhttp://dx.doi.org/10.1089/cmb.2009.0275
ISI Accession Number IDWOS:000285965600008
ReferencesReferences in Scopus
DC Field
Value
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
2011 Impact Factor: 1.546
2011 SCImago Journal Rankings: 0.263
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
Author Affiliations
  1. The University of Hong Kong
  2. National University of Singapore