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
2011 Impact Factor: 4.092
2011 SCImago Journal Rankings: 0.519
DOIhttp://dx.doi.org/10.1371/journal.pone.0012848
ISI Accession Number IDWOS:000282210700003
PubMed Central IDPMC2946929
ReferencesReferences in Scopus
DC Field
Value
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
2011 Impact Factor: 4.092
2011 SCImago Journal Rankings: 0.519
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
Author Affiliations
  1. The University of Hong Kong
  2. National University of Singapore