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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
2013 SCImago Journal Rankings: 0.310
 
DOIhttp://dx.doi.org/10.1007/978-3-642-04241-6_33
 
ReferencesReferences in Scopus
 
DC FieldValue
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
2013 SCImago Journal Rankings: 0.310
 
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
 
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Author Affiliations
  1. The University of Hong Kong
  2. National University of Singapore