siDRM: an effective and generally applicable online siRNA design tool

Bioinformatics
Wuming GongTongbin Li

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.

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Citations

Jul 9, 2011·Journal of Chemical Information and Modeling·Takeshi Kawabata
Feb 18, 2014·Nucleic Acid Therapeutics·Sun Woo HongDong-ki Lee
Nov 11, 2008·Nucleic Acids Research·Yongliang RenTongbin Li
Apr 3, 2010·Nucleic Acids Research·Walter R StrappsSteven R Bartz
Apr 17, 2013·Neurotherapeutics : the Journal of the American Society for Experimental NeuroTherapeutics·Pavitra S RamachandranBeverly L Davidson
Mar 1, 2011·Expert Opinion on Drug Discovery·Meenakshi MalhotraSatya Prakash
Jan 5, 2016·International Journal of Medical Informatics·Katrina M RomagnoliHarry Hochheiser
Dec 15, 2010·Biochemical and Biophysical Research Communications·Aparna ChaudharySanjeev Garg
Jun 4, 2010·Current Protocols in Cell Biology·Kumi SakuraiJohn J Rossi
Apr 3, 2019·Cold Spring Harbor Protocols·Chengjian Li, Phillip D Zamore
Nov 2, 2019·Experimental Neurology·Almudena PachecoGianluca Gallo
Jul 22, 2021·RNA Biology·Anton ZhiyanovAlexander Tonevitsky

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