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Article: Structural alignment of RNA with triple helix structure

TitleStructural alignment of RNA with triple helix structure
Authors
Issue Date2012
PublisherMary Ann Liebert, Inc Publishers. The Journal's web site is located at http://www.liebertpub.com/cmb
Citation
Journal of Computational Biology, 2012, v. 19 n. 4, p. 365-378 How to Cite?
AbstractStructural alignment is useful in identifying members of ncRNAs. Existing tools are all based on the secondary structures of the molecules. There is evidence showing that tertiary interactions (the interaction between a single-stranded nucleotide and a base-pair) in triple helix structures are critical in some functions of ncRNAs. In this article, we address the problem of structural alignment of RNAs with the triple helix. We provide a formal definition to capture a simplified model of a triple helix structure, then develop an algorithm of O(mn(3)) time to align a query sequence (of length m) with known triple helix structure with a target sequence (of length n) with an unknown structure. The resulting algorithm is shown to be useful in identifying ncRNA members in a simulated genome. © Copyright 2012, Mary Ann Liebert, Inc. 2012.
Persistent Identifierhttp://hdl.handle.net/10722/165843
ISSN
2015 Impact Factor: 1.537
2015 SCImago Journal Rankings: 1.615
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorWong, TKFen_US
dc.contributor.authorYiu, SMen_US
dc.date.accessioned2012-09-20T08:24:28Z-
dc.date.available2012-09-20T08:24:28Z-
dc.date.issued2012en_US
dc.identifier.citationJournal of Computational Biology, 2012, v. 19 n. 4, p. 365-378en_US
dc.identifier.issn1066-5277-
dc.identifier.urihttp://hdl.handle.net/10722/165843-
dc.description.abstractStructural alignment is useful in identifying members of ncRNAs. Existing tools are all based on the secondary structures of the molecules. There is evidence showing that tertiary interactions (the interaction between a single-stranded nucleotide and a base-pair) in triple helix structures are critical in some functions of ncRNAs. In this article, we address the problem of structural alignment of RNAs with the triple helix. We provide a formal definition to capture a simplified model of a triple helix structure, then develop an algorithm of O(mn(3)) time to align a query sequence (of length m) with known triple helix structure with a target sequence (of length n) with an unknown structure. The resulting algorithm is shown to be useful in identifying ncRNA members in a simulated genome. © Copyright 2012, Mary Ann Liebert, Inc. 2012.-
dc.languageengen_US
dc.publisherMary Ann Liebert, Inc Publishers. The Journal's web site is located at http://www.liebertpub.com/cmb-
dc.relation.ispartofJournal of Computational Biologyen_US
dc.rightsThis is a copy of an article published in the Journal of Computational Biology © 2012 copyright Mary Ann Liebert, Inc.; Journal of Computational Biology is available online at: http://www.liebertonline.com.-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.meshAlgorithms-
dc.subject.meshNucleic Acid Conformation-
dc.subject.meshRNA, Untranslated - chemistry-
dc.subject.meshSequence Alignment - methods-
dc.subject.meshSequence Analysis, RNA - methods-
dc.titleStructural alignment of RNA with triple helix structureen_US
dc.typeArticleen_US
dc.identifier.emailWong, TKF: kfwong@cs.hku.hken_US
dc.identifier.emailYiu, SM: smyiu@cs.hku.hken_US
dc.identifier.authorityYiu, SM=rp00207en_US
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1089/cmb.2010.0052-
dc.identifier.pmid22468707-
dc.identifier.scopuseid_2-s2.0-84859371545-
dc.identifier.hkuros208101en_US
dc.identifier.volume19en_US
dc.identifier.issue4-
dc.identifier.spage365en_US
dc.identifier.epage378en_US
dc.identifier.isiWOS:000302553800003-
dc.publisher.placeUnited States-

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