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dc.contributor.authorM. Chalk, Alistair
dc.contributor.authorL. L. Sonnhammer, Erik
dc.date.accessioned2017-05-03T15:23:14Z
dc.date.available2017-05-03T15:23:14Z
dc.date.issued2008
dc.date.modified2009-11-06T05:53:27Z
dc.identifier.issn13674803
dc.identifier.doi10.1093/bioinformatics/btn121
dc.identifier.urihttp://hdl.handle.net/10072/26429
dc.description.abstractArtificially synthesized short interfering RNAs (siRNAs) are widely used in functional genomics to knock down specific target genes. One ongoing challenge is to guarantee that the siRNA does not elicit off-target effects. Initial reports suggested that siRNAs were highly sequence-specific; however, subsequent data indicates that this is not necessarily the case. It is still uncertain what level of similarity and other rules are required for an off-target effect to be observed, and scoring schemes have not been developed to look beyond simple measures such as the number of mismatches or the number of consecutive matching bases present. We created design rules for predicting the likelihood of a non-specific effect and present a web server that allows the user to check the specificity of a given siRNA in a flexible manner using a combination of methods. The server finds potential off-target matches in the corresponding RefSeq database and ranks them according to a scoring system based on experimental studies of specificity. AVAILABILITY: The server is available at http://informatics-eskitis.griffith.edu.au/SpecificityServer.
dc.description.peerreviewedYes
dc.description.publicationstatusYes
dc.languageEnglish
dc.language.isoen_AU
dc.publisherOxford University Press
dc.publisher.placeUnited Kingdom
dc.publisher.urihttp://bioinformatics.oxfordjournals.org/
dc.relation.ispartofstudentpublicationN
dc.relation.ispartofpagefrom1316
dc.relation.ispartofpageto1317
dc.relation.ispartofissue10
dc.relation.ispartofjournalBioinformatics
dc.relation.ispartofvolume24
dc.rights.retentionN
dc.subject.fieldofresearchBioinformatics
dc.subject.fieldofresearchMathematical Sciences
dc.subject.fieldofresearchBiological Sciences
dc.subject.fieldofresearchInformation and Computing Sciences
dc.subject.fieldofresearchcode060102
dc.subject.fieldofresearchcode01
dc.subject.fieldofresearchcode06
dc.subject.fieldofresearchcode08
dc.titlesiRNA specificity searching incorporating mismatch tolerance data
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
gro.date.issued2008
gro.hasfulltextNo Full Text
gro.griffith.authorChalk, Alistair M.


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