Conference Paper: 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
Yiu, SM1
KeywordsNon-coding RNA
Pseudoknots
Structural alignment
Issue Date2009
PublisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/
CitationLecture Notes In Computer Science (Including Subseries Lecture Notes In Artificial Intelligence And Lecture Notes In Bioinformatics), 2009, v. 5724 LNBI, p. 403-414 [How to Cite?]
DOI: http://dx.doi.org/10.1007/978-3-642-04241-6_33
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 paper, 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 cover all known ncRNAs in both Rfam and PseudoBase databases. A preliminary evaluation on our algorithms show that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA. © 2009 Springer Berlin Heidelberg.
Description9th International Workshop on Algorithms in Bioinformatics (WABI), Philadelphia, PA, USA, 12-13 September 2009.
ISSN0302-9743
2011 SCImago Journal Rankings: 0.034
DOIhttp://dx.doi.org/10.1007/978-3-642-04241-6_33
ReferencesReferences in Scopus
DC Field
Value
dc.contributor.authorWong, TKF
dc.contributor.authorLam, TW
dc.contributor.authorSung, WK
dc.contributor.authorYiu, SM
dc.date.accessioned2010-09-25T14:50:44Z
dc.date.available2010-09-25T14:50:44Z
dc.date.issued2009
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 paper, 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 cover all known ncRNAs in both Rfam and PseudoBase databases. A preliminary evaluation on our algorithms show that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA. © 2009 Springer Berlin Heidelberg.
dc.description.natureLink_to_subscribed_fulltext
dc.description9th International Workshop on Algorithms in Bioinformatics (WABI), Philadelphia, PA, USA, 12-13 September 2009.
dc.identifier.citationLecture Notes In Computer Science (Including Subseries Lecture Notes In Artificial Intelligence And Lecture Notes In Bioinformatics), 2009, v. 5724 LNBI, p. 403-414 [How to Cite?]
DOI: http://dx.doi.org/10.1007/978-3-642-04241-6_33
dc.identifier.doihttp://dx.doi.org/10.1007/978-3-642-04241-6_33
dc.identifier.epage414
dc.identifier.hkuros161351
dc.identifier.issn0302-9743
2011 SCImago Journal Rankings: 0.034
dc.identifier.openurl
dc.identifier.scopuseid_2-s2.0-70350385107
dc.identifier.spage403
dc.identifier.urihttp://hdl.handle.net/10722/93095
dc.identifier.volume5724 LNBI
dc.languageeng
dc.publisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/
dc.publisher.placeGermany
dc.relation.ispartofLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
dc.relation.referencesReferences in Scopus
dc.rightsThe original publication is available at www.springerlink.com
dc.subjectNon-coding RNA
dc.subjectPseudoknots
dc.subjectStructural alignment
dc.titleStructural alignment of RNA with complex pseudoknot structure
dc.typeConference_Paper
Author Affiliations
  1. The University of Hong Kong
  2. National University of Singapore