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Bioinformatics Advance Access originally published online on April 7, 2008
Bioinformatics 2008 24(10):1316-1317; doi:10.1093/bioinformatics/btn121
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

siRNA specificity searching incorporating mismatch tolerance data

Alistair M. Chalk 1 and Erik L. L. Sonnhammer 1,2,*

1Department of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm and 2Stockholm Bioinformatics Center, Stockholm University, S-106 91 Stockholm, Sweden

*To whom correspondence should be addressed.


  Abstract

Artificially 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.

Contact: Erik.Sonnhammer{at}sbc.su.se

Supplementary information: Supplementary analysis and figures are available at Bioinformatics online.

Associate Editor: Trey Ideker

Received on November 16, 2007; revised on March 11, 2008; accepted on April 3, 2008

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