title: siDRM: an effective and generally applicable online siRNA design tool.
abstract: 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.
authors: Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA.
authors: Wuming
authors: W
authors: Gong
authors: Yongliang
authors: Y
authors: Ren
authors: Haiyan
authors: H
authors: Zhou
authors: Yejun
authors: Y
authors: Wang
authors: Shuli
authors: S
authors: Kang
authors: Tongbin
authors: T
authors: Li
mesh_terms: D000465:Algorithms; D030561:Databases, Nucleic Acid; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000737:chemistry*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D034741:RNA, Small Interfering