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Article: Adjacent nucleotide dependence in ncRNA and order-1 SCFG for ncRNA identification
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TitleAdjacent nucleotide dependence in ncRNA and order-1 SCFG for ncRNA identification
 
AuthorsWong, TKF1
Lam, TW1
Sung, WK2
Yiu, SM1
 
Issue Date2010
 
PublisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.action
 
CitationPlos One, 2010, v. 5 n. 9 [How to Cite?]
DOI: http://dx.doi.org/10.1371/journal.pone.0012848
 
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.
 
ISSN1932-6203
2012 Impact Factor: 3.73
2012 SCImago Journal Rankings: 1.512
 
DOIhttp://dx.doi.org/10.1371/journal.pone.0012848
 
PubMed Central IDPMC2946929
 
ISI Accession Number IDWOS:000282210700003
 
ReferencesReferences in Scopus
 
DC FieldValue
dc.contributor.authorWong, TKF
 
dc.contributor.authorLam, TW
 
dc.contributor.authorSung, WK
 
dc.contributor.authorYiu, SM
 
dc.date.accessioned2011-09-23T06:19:28Z
 
dc.date.available2011-09-23T06:19:28Z
 
dc.date.issued2010
 
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.
 
dc.description.naturepublished_or_final_version
 
dc.identifier.citationPlos One, 2010, v. 5 n. 9 [How to Cite?]
DOI: http://dx.doi.org/10.1371/journal.pone.0012848
 
dc.identifier.citeulike7926889
 
dc.identifier.doihttp://dx.doi.org/10.1371/journal.pone.0012848
 
dc.identifier.epagee12848
 
dc.identifier.hkuros192235
 
dc.identifier.isiWOS:000282210700003
 
dc.identifier.issn1932-6203
2012 Impact Factor: 3.73
2012 SCImago Journal Rankings: 1.512
 
dc.identifier.issue9
 
dc.identifier.pmcidPMC2946929
 
dc.identifier.pmid20927402
 
dc.identifier.scopuseid_2-s2.0-77958557836
 
dc.identifier.spagee12848
 
dc.identifier.urihttp://hdl.handle.net/10722/140796
 
dc.identifier.volume5
 
dc.languageeng
 
dc.publisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.action
 
dc.publisher.placeUnited States
 
dc.relation.ispartofPLoS ONE
 
dc.relation.referencesReferences in Scopus
 
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 identification
 
dc.typeArticle
 
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Author Affiliations
  1. The University of Hong Kong
  2. National University of Singapore