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Conference Paper: Local structural alignment of RNA with affine gap model

TitleLocal structural alignment of RNA with affine gap model
Authors
KeywordsAffine Gap
Local Structural Alignment
Non-Coding Rna
Issue Date2010
PublisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/
Citation
The 6th International Symposium (ISBRA 2010), Storrs, CT., 23-26 May 2010. In Lecture Notes In Computer Science, 2010, v. 6053, p. 191-202 How to Cite?
AbstractPredicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps. In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem. Based on a preliminary experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model. © 2010 Springer-Verlag Berlin Heidelberg.
DescriptionLNCS v. 6053 entitled: Bioinformatics Research and Applications: 6th International Symposium, ISBRA 2010, Storrs, CT, USA, May 23-26, 2010. Proceedings
Persistent Identifierhttp://hdl.handle.net/10722/151971
ISSN
2005 Impact Factor: 0.402
2015 SCImago Journal Rankings: 0.252
References

 

DC FieldValueLanguage
dc.contributor.authorWong, TKFen_US
dc.contributor.authorCheung, BWYen_US
dc.contributor.authorLam, TWen_US
dc.contributor.authorYiu, SMen_US
dc.date.accessioned2012-06-26T06:31:41Z-
dc.date.available2012-06-26T06:31:41Z-
dc.date.issued2010en_US
dc.identifier.citationThe 6th International Symposium (ISBRA 2010), Storrs, CT., 23-26 May 2010. In Lecture Notes In Computer Science, 2010, v. 6053, p. 191-202en_US
dc.identifier.issn0302-9743en_US
dc.identifier.urihttp://hdl.handle.net/10722/151971-
dc.descriptionLNCS v. 6053 entitled: Bioinformatics Research and Applications: 6th International Symposium, ISBRA 2010, Storrs, CT, USA, May 23-26, 2010. Proceedings-
dc.description.abstractPredicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps. In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem. Based on a preliminary experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model. © 2010 Springer-Verlag Berlin Heidelberg.en_US
dc.languageengen_US
dc.publisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/en_US
dc.relation.ispartofLecture Notes in Computer Scienceen_US
dc.subjectAffine Gapen_US
dc.subjectLocal Structural Alignmenten_US
dc.subjectNon-Coding Rnaen_US
dc.titleLocal structural alignment of RNA with affine gap modelen_US
dc.typeConference_Paperen_US
dc.identifier.emailLam, TW:twlam@cs.hku.hken_US
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_US
dc.identifier.authorityLam, TW=rp00135en_US
dc.identifier.authorityYiu, SM=rp00207en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1007/978-3-642-13078-6_22en_US
dc.identifier.scopuseid_2-s2.0-77953802882en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-77953802882&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume6053en_US
dc.identifier.spage191en_US
dc.identifier.epage202en_US
dc.publisher.placeGermanyen_US
dc.identifier.scopusauthoridWong, TKF=25423289800en_US
dc.identifier.scopusauthoridCheung, BWY=8434373700en_US
dc.identifier.scopusauthoridLam, TW=7202523165en_US
dc.identifier.scopusauthoridYiu, SM=7003282240en_US
dc.customcontrol.immutablesml 151014-

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