siDRM is an implementation of the DRM rule sets for selecting effective siRNAs. These rule sets were obtained in the following three steps: (1) A survey of significant features was conducted on the large and diverse dataset compiled from siRecords, with all known features implicated to have impacts on the siRNA efficacy. This survey resulted in a list of features associated with a significant up-shift of the siRNA efficacy distribution, and/or significantly boosting the chances of achieving higher siRNA efficacy. (2) A feature combination analysis was performed to exploit the positive cooperativity of the significant features identified in their joint effects in boosting the siRNA efficacy. A list of feature combinations (also called rules) leading to substantial improvement in efficacy in the training dataset was obtained. (3) The DRM (or disjunctive rule merging) algorithm was applied to merge and reorganize the rules obtained, resulting in a bundle of rule sets (or disjunctions of rules), ordered descendingly in stringency.

   • Ren, Y., Gong, W., Xu, Q., Zheng, X., Lin, D., Wang, Y. and Li, T. (2006) siRecords: an extensive database of mammalian siRNAs with efficacy ratings. Bioinformatics , 22, 1027-1028. [PubMed]
   • Gong, W., Ren, Y., Xu, Q., Wang, Y., Lin, D., Zhou, H. and Li, T. (2006) Integrated siRNA design based on surveying of features associated with high RNAi effectiveness. BMC Bioinformatics , 7 , 516. [PubMed] [Full text]
   • Gong, W., Ren, Y., Zhou, H., Wang, Y., Kang, S. and Li, T. (2008) siDRM: an effective and generally applicable online siRNA design tool. Bioinformatics , 24 , 2405-2406. [PubMed]
   • Ren, Y., Gong, W., Zhou, H., Wang, Y., Xiao, F. and Li, T. (2009) siRecords: a database of mammalian RNAi experiments and efficacies. Nucleic Acids Res , 37 , D146-149. [PubMed] [Full text]

• Ambion siRNA Target Finder , Ambion, Inc.
• Jack Lin's siRNA Sequence Finder , Cold Spring Harbor Laboratory.
• siDESIGN Center , Dharmacon, Inc.
• siRNA Target Finder , GenScript Corp.
• Imgenex sirna Designer , Imgenex Corp.
• EMBOSS sirna , Institute Pasteur .
• IDT RNAi Design (SciTools) , Integrated DNA Technologies, Inc.
• BLOCK-iT RNAi Designer , Invitrogen Corp.
• siSearch , Karolinska Institutet.
• DSIR , Mines Institute of Paris.
• SiMAX , MWG-Biotech, Inc.
• ThermoComposition19 , National Institutes of Health.
• BIOPREDsi , Novartis Institutes for BioMedical Research.
• SiDE , Prince Felipe Research Centre.
• Promega siRNA Target Designer , Promega Corp.
• QIAGEN siRNA Design Tool , QIAGEN, Inc.
• SDS/MPI , University of Hong Kong.
• siDRM , Biolead.org.
• OptiRNA , University of Nebraska-Lincoln.
• siRNArules 1.0 , University of Oslo.
• Sirna , Wadsworth Bioinformatics Center.
• WI siRNA Selection Program , Whitehead Institute.
• siRNA selector , Wistar Institute.