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Conference Paper: Prediction of minimum free energy structure for simple non-standard pseudoknot

TitlePrediction of minimum free energy structure for simple non-standard pseudoknot
Authors
KeywordsComplex Pseudoknot
Rna
Secondary Structure Prediction
Simple Non-Standard Pseudoknot
Issue Date2011
Citation
Communications In Computer And Information Science, 2011, v. 127 CCIS, p. 345-355 How to Cite?
AbstractPredicting the secondary structure with minimum free energy of an RNA molecule is an important problem in computational biology. Unfortunately, the problem is in general NP-hard if there are pseudoknots in the structure. Existing algorithms usually target at some restricted classes of pseudoknots. In this paper, we extend the current classification of pseudoknots to capture more complicated pseudoknots, namely the simple non-standard pseudoknots of degree k. We provide an algorithm to compute the structure with minimum free energy for this type of pseudoknots of degree 4 which covers all known secondary structures of RNAs in this class. Our algorithm runs in O(m 4) time where m is the length of the input RNA sequence. © 2011 Springer-Verlag Berlin Heidelberg.
Persistent Identifierhttp://hdl.handle.net/10722/151995
ISSN
2015 SCImago Journal Rankings: 0.149
References

 

DC FieldValueLanguage
dc.contributor.authorWong, TKFen_US
dc.contributor.authorYiu, SMen_US
dc.date.accessioned2012-06-26T06:32:13Z-
dc.date.available2012-06-26T06:32:13Z-
dc.date.issued2011en_US
dc.identifier.citationCommunications In Computer And Information Science, 2011, v. 127 CCIS, p. 345-355en_US
dc.identifier.issn1865-0929en_US
dc.identifier.urihttp://hdl.handle.net/10722/151995-
dc.description.abstractPredicting the secondary structure with minimum free energy of an RNA molecule is an important problem in computational biology. Unfortunately, the problem is in general NP-hard if there are pseudoknots in the structure. Existing algorithms usually target at some restricted classes of pseudoknots. In this paper, we extend the current classification of pseudoknots to capture more complicated pseudoknots, namely the simple non-standard pseudoknots of degree k. We provide an algorithm to compute the structure with minimum free energy for this type of pseudoknots of degree 4 which covers all known secondary structures of RNAs in this class. Our algorithm runs in O(m 4) time where m is the length of the input RNA sequence. © 2011 Springer-Verlag Berlin Heidelberg.en_US
dc.languageengen_US
dc.relation.ispartofCommunications in Computer and Information Scienceen_US
dc.subjectComplex Pseudoknoten_US
dc.subjectRnaen_US
dc.subjectSecondary Structure Predictionen_US
dc.subjectSimple Non-Standard Pseudoknoten_US
dc.titlePrediction of minimum free energy structure for simple non-standard pseudoknoten_US
dc.typeConference_Paperen_US
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_US
dc.identifier.authorityYiu, SM=rp00207en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1007/978-3-642-18472-7_27en_US
dc.identifier.scopuseid_2-s2.0-79952499286en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-79952499286&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume127 CCISen_US
dc.identifier.spage345en_US
dc.identifier.epage355en_US
dc.identifier.scopusauthoridWong, TKF=25423289800en_US
dc.identifier.scopusauthoridYiu, SM=7003282240en_US

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