Journal Article

<i>siDRM</i>: an effective and generally applicable online siRNA design tool

Wuming Gong, Yongliang Ren, Haiyan Zhou, Yejun Wang, Shuli Kang and Tongbin Li

in Bioinformatics

Volume 24, issue 20, pages 2405-2406
Published in print October 2008 | ISSN: 1367-4803
Published online August 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn442
siDRM: an effective and generally applicable online siRNA design tool

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Summary: Small interfering RNAs (siRNAs) have become an indispensable tool for the investigation of gene functions. Most existing siRNA design tools were trained on datasets assembled from confined origins, incompatible with the diverse siRNA laboratory practice to which these tools will ultimately be applied. We have performed an updated analysis using the disjunctive rule merging (DRM) approach on a large and diverse dataset compiled from siRecords, and implemented the resulting rule sets in siDRM, a new online siRNA design tool. siDRM also implements a few high-sensitivity rule sets and fast rule sets, links to siRecords, and uses several filters to check unwanted detrimental effects, including innate immune responses, cell toxic effects and off-target activities in selecting siRNAs. A performance comparison using an independent dataset indicated that siDRM outperforms 19 existing siRNA design tools in identifying effective siRNAs.

Availability: siDRM can be accessed at http://siRecords.umn.edu/siDRM/.

Contact: toli@biocompute.umn.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1470 words. 

Subjects: Bioinformatics and Computational Biology

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