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Conference Paper: Structural alignment of RNA with complex pseudoknot structure

TitleStructural alignment of RNA with complex pseudoknot structure
Authors
KeywordsNon-coding RNA
Pseudoknots
Structural alignment
Issue Date2009
PublisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/
Citation
Lecture 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?
Abstract
The 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.
Persistent Identifierhttp://hdl.handle.net/10722/93095
ISSN
2013 SCImago Journal Rankings: 0.310
References

 

DC FieldValueLanguage
dc.contributor.authorWong, TKFen_HK
dc.contributor.authorLam, TWen_HK
dc.contributor.authorSung, WKen_HK
dc.contributor.authorYiu, SMen_HK
dc.date.accessioned2010-09-25T14:50:44Z-
dc.date.available2010-09-25T14:50:44Z-
dc.date.issued2009en_HK
dc.identifier.citationLecture Notes In Computer Science (Including Subseries Lecture Notes In Artificial Intelligence And Lecture Notes In Bioinformatics), 2009, v. 5724 LNBI, p. 403-414en_HK
dc.identifier.issn0302-9743en_HK
dc.identifier.urihttp://hdl.handle.net/10722/93095-
dc.description9th International Workshop on Algorithms in Bioinformatics (WABI), Philadelphia, PA, USA, 12-13 September 2009.-
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.en_HK
dc.languageengen_HK
dc.publisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/en_HK
dc.relation.ispartofLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)en_HK
dc.rightsThe original publication is available at www.springerlink.com-
dc.subjectNon-coding RNAen_HK
dc.subjectPseudoknotsen_HK
dc.subjectStructural alignmenten_HK
dc.titleStructural alignment of RNA with complex pseudoknot structureen_HK
dc.typeConference_Paperen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0302-9743&volume=5724&spage=403&epage=414&date=2009&atitle=Structural+alignment+of+RNA+with+complex+pseudoknot+structure-
dc.identifier.emailLam, TW:twlam@cs.hku.hken_HK
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_HK
dc.identifier.authorityLam, TW=rp00135en_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1007/978-3-642-04241-6_33en_HK
dc.identifier.scopuseid_2-s2.0-70350385107en_HK
dc.identifier.hkuros161351en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-70350385107&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume5724 LNBIen_HK
dc.identifier.spage403en_HK
dc.identifier.epage414en_HK
dc.publisher.placeGermanyen_HK
dc.identifier.scopusauthoridWong, TKF=25423289800en_HK
dc.identifier.scopusauthoridLam, TW=7202523165en_HK
dc.identifier.scopusauthoridSung, WK=13310059700en_HK
dc.identifier.scopusauthoridYiu, SM=7003282240en_HK

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