Bioinformatics Advance Access originally published online on August 20, 2008
Bioinformatics 2008 24(20):2405-2406; doi:10.1093/bioinformatics/btn442
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siDRM: an effective and generally applicable online siRNA design tool
Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
*To whom correspondence should be addressed.
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Abstract |
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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{at}biocompute.umn.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Associate Editor: Jonathan Wren
Received on March 10, 2008; revised on August 17, 2008; accepted on August 17, 2008
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