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) |
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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 |
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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 |
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Homology search by WU-BLAST |
Chalk and Sonnhammer (2008) |