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Article: Adjacent nucleotide dependence in ncRNA and order-1 SCFG for ncRNA identification

TitleAdjacent nucleotide dependence in ncRNA and order-1 SCFG for ncRNA identification
Authors
Issue Date2010
PublisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.action
Citation
Plos One, 2010, v. 5 n. 9 How to Cite?
AbstractBackground: Non-coding RNAs (ncRNAs) are known to be involved in many critical biological processes, and identification of ncRNAs is an important task in biological research. A popular software, Infernal, is the most successful prediction tool and exhibits high sensitivity. The application of Infernal has been mainly focused on small suspected regions. We tried to apply Infernal on a chromosome level; the results have high sensitivity, yet contain many false positives. Further enhancing Infernal for chromosome level or genome wide study is desirable. Methodology: Based on the conjecture that adjacent nucleotide dependence affects the stability of the secondary structure of an ncRNA, we first conduct a systematic study on human ncRNAs and find that adjacent nucleotide dependence in human ncRNA should be useful for identifying ncRNAs. We then incorporate this dependence in the SCFG model and develop a new order-1 SCFG model for identifying ncRNAs. Conclusions: With respect to our experiments on human chromosomes, the proposed new model can eliminate more than 50% false positives reported by Infernal while maintaining the same sensitivity. The executable and the source code of programs are freely available at http://i.cs.hku.hk/~kfwong/order1scfg. © 2010 Wong et al.
Persistent Identifierhttp://hdl.handle.net/10722/140796
ISSN
2014 Impact Factor: 3.234
2014 SCImago Journal Rankings: 1.300
PubMed Central ID
ISI Accession Number ID
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.accessioned2011-09-23T06:19:28Z-
dc.date.available2011-09-23T06:19:28Z-
dc.date.issued2010en_HK
dc.identifier.citationPlos One, 2010, v. 5 n. 9en_HK
dc.identifier.issn1932-6203en_HK
dc.identifier.urihttp://hdl.handle.net/10722/140796-
dc.description.abstractBackground: Non-coding RNAs (ncRNAs) are known to be involved in many critical biological processes, and identification of ncRNAs is an important task in biological research. A popular software, Infernal, is the most successful prediction tool and exhibits high sensitivity. The application of Infernal has been mainly focused on small suspected regions. We tried to apply Infernal on a chromosome level; the results have high sensitivity, yet contain many false positives. Further enhancing Infernal for chromosome level or genome wide study is desirable. Methodology: Based on the conjecture that adjacent nucleotide dependence affects the stability of the secondary structure of an ncRNA, we first conduct a systematic study on human ncRNAs and find that adjacent nucleotide dependence in human ncRNA should be useful for identifying ncRNAs. We then incorporate this dependence in the SCFG model and develop a new order-1 SCFG model for identifying ncRNAs. Conclusions: With respect to our experiments on human chromosomes, the proposed new model can eliminate more than 50% false positives reported by Infernal while maintaining the same sensitivity. The executable and the source code of programs are freely available at http://i.cs.hku.hk/~kfwong/order1scfg. © 2010 Wong et al.en_HK
dc.languageengen_US
dc.publisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.actionen_HK
dc.relation.ispartofPLoS ONEen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.meshComputational Biology - methods-
dc.subject.meshMolecular Sequence Data-
dc.subject.meshNucleic Acid Conformation-
dc.subject.meshNucleotides - chemistry - genetics-
dc.subject.meshRNA, Untranslated - chemistry - genetics-
dc.titleAdjacent nucleotide dependence in ncRNA and order-1 SCFG for ncRNA identificationen_HK
dc.typeArticleen_HK
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.naturepublished_or_final_version-
dc.identifier.doi10.1371/journal.pone.0012848en_HK
dc.identifier.pmid20927402en_HK
dc.identifier.pmcidPMC2946929-
dc.identifier.scopuseid_2-s2.0-77958557836en_HK
dc.identifier.hkuros192235en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-77958557836&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume5en_HK
dc.identifier.issue9en_HK
dc.identifier.spagee12848en_US
dc.identifier.epagee12848en_US
dc.identifier.isiWOS:000282210700003-
dc.publisher.placeUnited Statesen_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
dc.identifier.citeulike7926889-

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