File Download
  Links for fulltext
     (May Require Subscription)
Supplementary

Article: Filtering of ineffective siRNAs and improved siRNA design tool

TitleFiltering of ineffective siRNAs and improved siRNA design tool
Authors
Issue Date2005
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
Bioinformatics, 2005, v. 21 n. 2, p. 144-151 How to Cite?
AbstractMotivation: Short interfering RNAs (siRNAs) can be used to suppress gene expression and possess many potential applications in therapy, but how to design an effective siRNA is still not clear. Based on the MPI (Max-Planck-Institute) basic principles, a number of siRNA design tools have been developed recently. The set of candidates reported by these tools is usually large and often contains ineffective siRNAs. In view of this, we initiate the study of filtering ineffective siRNAs. Results: The contribution of this paper is 2-fold. First, we propose a fair scheme to compare existing design tools based on real data in the literature. Second, we attempt to improve the MPI principles and existing tools by an algorithm that can filter ineffective siRNAs. The algorithm is based on some new observations on the secondary structure, which we have verified by AI techniques (decision trees and support vector machines). We have tested our algorithm together with the MPI principles and the existing tools. The results show that our filtering algorithm is effective. © Oxford University Press 2004; all rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/43623
ISSN
2015 Impact Factor: 5.766
2015 SCImago Journal Rankings: 4.643
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorYiu, SMen_HK
dc.contributor.authorWong, PWHen_HK
dc.contributor.authorLam, TWen_HK
dc.contributor.authorMui, YCen_HK
dc.contributor.authorKung, HFen_HK
dc.contributor.authorLin, Men_HK
dc.contributor.authorCheung, YTen_HK
dc.date.accessioned2007-03-23T04:50:42Z-
dc.date.available2007-03-23T04:50:42Z-
dc.date.issued2005en_HK
dc.identifier.citationBioinformatics, 2005, v. 21 n. 2, p. 144-151en_HK
dc.identifier.issn1367-4803en_HK
dc.identifier.urihttp://hdl.handle.net/10722/43623-
dc.description.abstractMotivation: Short interfering RNAs (siRNAs) can be used to suppress gene expression and possess many potential applications in therapy, but how to design an effective siRNA is still not clear. Based on the MPI (Max-Planck-Institute) basic principles, a number of siRNA design tools have been developed recently. The set of candidates reported by these tools is usually large and often contains ineffective siRNAs. In view of this, we initiate the study of filtering ineffective siRNAs. Results: The contribution of this paper is 2-fold. First, we propose a fair scheme to compare existing design tools based on real data in the literature. Second, we attempt to improve the MPI principles and existing tools by an algorithm that can filter ineffective siRNAs. The algorithm is based on some new observations on the secondary structure, which we have verified by AI techniques (decision trees and support vector machines). We have tested our algorithm together with the MPI principles and the existing tools. The results show that our filtering algorithm is effective. © Oxford University Press 2004; all rights reserved.en_HK
dc.format.extent166819 bytes-
dc.format.extent26112 bytes-
dc.format.mimetypeapplication/pdf-
dc.format.mimetypeapplication/msword-
dc.languageengen_HK
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/en_HK
dc.relation.ispartofBioinformaticsen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.meshAlgorithmsen_HK
dc.subject.meshArtificial intelligenceen_HK
dc.subject.meshComputer-aided designen_HK
dc.subject.meshModels, molecularen_HK
dc.subject.meshSequence analysis, rnaen_HK
dc.titleFiltering of ineffective siRNAs and improved siRNA design toolen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1471-2105&volume=21&issue=2&spage=144&epage=151&date=2005&atitle=Filtering+of+ineffective+siRNAs+and+improved+siRNA+design+toolen_HK
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_HK
dc.identifier.emailLam, TW:twlam@cs.hku.hken_HK
dc.identifier.emailLin, M:mcllin@hkucc.hku.hken_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.identifier.authorityLam, TW=rp00135en_HK
dc.identifier.authorityLin, M=rp00746en_HK
dc.description.naturepublished_or_final_versionen_HK
dc.identifier.doi10.1093/bioinformatics/bth498en_HK
dc.identifier.pmid15333460-
dc.identifier.scopuseid_2-s2.0-13444282536en_HK
dc.identifier.hkuros102721-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-13444282536&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume21en_HK
dc.identifier.issue2en_HK
dc.identifier.spage144en_HK
dc.identifier.epage151en_HK
dc.identifier.isiWOS:000226308500002-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridYiu, SM=7003282240en_HK
dc.identifier.scopusauthoridWong, PWH=9734871500en_HK
dc.identifier.scopusauthoridLam, TW=7202523165en_HK
dc.identifier.scopusauthoridMui, YC=16638793300en_HK
dc.identifier.scopusauthoridKung, HF=7402514190en_HK
dc.identifier.scopusauthoridLin, M=7404816359en_HK
dc.identifier.scopusauthoridCheung, YT=36911126100en_HK
dc.identifier.citeulike78315-

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats