Table 1.

Small interfering RNA design software programs.

Website	URL	Developer	Features	Rules	Elimination of off-target effect	Reference
AsiDesigner	http://sysbio.kribb.re.kr:8080/AsiDesigner/menuDesigner.jsf	Bioinformatics Research Center, KRIBB	Exon-based siRNA design algorithm considering alternative splicing and mRNA secondary structure	G/C content, maximum consecutive bases, existence of single nucleotide polymorphism (SNP), self-alignment energy of siRNA	Homology search by BLAST and FASTA	Park et al. (2008)
DEQOR	http://bioinformatics.age.mpg.de/bioinformatics/DEQOR.html	MPI-AGE	Design and quality control of endoribonuclease-prepared small interfering RNAs (esiRNAs)		Homology search by BLAST	Henschel et al. (2004)
DSIR	http://biodev.cea.fr/DSIR/DSIR.html	Ecole des Mines de Paris	The publicly available siRNA datasets were used	Regarding importance of the presence of asymmetric short motifs in the siRNA sequence with A/U at the 5′ end and C/G at the 3′ end of the guide strand	Homology search by BLAST	Vert et al. (2006)
NEXT-RNAi	http://b110-wiki.dkfz.de/signaling/wiki/display/nextrnai/NEXT-RNAi	German Cancer Research Center (DKFZ)	Design a genome-wide siRNA library	Reynolds rule, Ui-Tei rule, Reynolds rule, Amarzguioui rule	Homology search by Bowtie	Horn et al. (2010)
OligoWalk	http://rna.urmc.rochester.edu/cgi-bin/server_exe/oligowalk/oligowalk_form.cgi	University of Rochester Medical Center	The secondary structures of the oligomer and target mRNA are considered based on thermodynamic parameters	Modified Reynolds rule	Homology search by BLAST	Lu and Mathews (2008)
OptiRNA	http://optirna.unl.edu/	University of Nebraska-Lincoln	Calculating thermodynamic features considering all possible secondary structures	Not considered	Not considered	Ladunga (2007)
OptiRNAi 2.0	http://rnai.nci.nih.gov/	National Institutes of Health	Rationally designed siRNA	Elbashir rule, Reynolds rule	Homology search by BLAST	Cui et al. (2004)
Sfold 2.2 (Srna)	http://sfold.wadsworth.org/cgi-bin/sirna.pl	Wadsworth Center, New York State Department of Health	Target accessibility evaluation is a unique feature. Uses Bayesian algorithm that is based on stacking energy rules but relaxes the need to specify the parameters	Reynolds rule	Homology search by BLAST	Ding et al. (2004)
siDirect 2.0	http://sidirect2.rnai.jp/	University of Tokyo	Empirically and rationally designed siRNA	Ui-Tei rule	Homology search by siDirect, and consider thermodynamic stability in the seed duplex	Naito et al. (2009)
siDRM	http://siRecords.umn.edu/siDRM/	University of Minnesota	A few high sensitivity rule sets and fast rule sets, links to siRecords were implemented and several filters to check unwanted detrimental effects, including innate immune responses, cell toxic effects, and off-target activities, were used			Gong et al. (2008)
sIR	http://biotools.swmed.edu/siRNA	University of Texas Southwestern Medical Center	Pre-designed siRNAs	Ui-Tei rule, Reynolds rule, Elbashir rule, Amarzguioui rule	Homology search by BLAST	Shah et al. (2007)
siRNA Selector (siRNA at WHITEHEAD)	http://sirna.wi.mit.edu/	Whitehead Institute for Biomedical Research	The siRNA design tool scans a target gene for candidate siRNA sequences that satisfy user-adjustable rules	Tuschl rule, Ui-Tei rule, Reynolds rule, Hsieh rule	Homology search by BLAST and WU-BLAST	Yuan et al. (2004)
SpecificityServer	http://informatics-eskitis.griffith.edu.au/SpecificityServer	Griffith University	A specificity scoring scheme		Homology search by WU-BLAST	Chalk and Sonnhammer (2008)