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Table 4 Comparison in performance between 15 online siRNA design tools and 4 DRM rule sets based on independent subset of Set T.

From: Integrated siRNA design based on surveying of features associated with high RNAi effectiveness

Design Program

Institution/Company

#Predicted effective siRNAs

#Predicted ineffective siRNAs

Sensitivity

Specificity

PPV (%)

Ambion siRNA Target Finder

Ambion, Inc.

144

80

0.645

0.362

74.3

Jack Lin's siRNA Sequence Finder

Cold Spring Harbor Laboratory

44

180

0.229

0.897

86.4

siDESIGN Center

Dharmacon, Inc.

7

217

0.036

0.983

85.7

siRNA Target Finder

GenScript Corp.

6

218

0.024

0.966

66.7

Imgenex sirna Designer

Imgenex Corp.

24

200

0.114

0.914

79.2

EMBOSS sirna

Institute Pasteur

180

44

0.801

0.190

73.8

IDT RNAi Design (SciTools)

Integrated DNA Technologies, Inc.

4

220

0.012

0.966

50.0

BLOCK-iT RNAi Designer

Invitrogen Corp.

2

222

0.012

1.000

100

siSearch

Karolinska Institutet

0

224

N/A

N/A

N/A

SiMAX

MWG-Biotech, Inc.

48

176

0.235

0.845

81.3

BIOPREDsi

Novartis Institutes for BioMedical Research

4

220

0.018

0.983

75.0

Promega siRNA Target Designer

Promega Corp.

26

198

0.127

0.914

80.8

QIAGEN siRNA Design Tool

QIAGEN, Inc.

33

191

0.151

0.862

75.8

SDS/MPI

University of Hong Kong

151

73

0.663

0.293

72.8

WI siRNA Selection Program

Whitehead Institute

12

212

0.072

1.000

100

DRM RS 0.951

 

1

223

0.006

1

100

DRM RS 0.895

 

4

220

0.024

1

100

DRM RS 0.845

 

5

219

0.030

1

100

DRM RS 0.827

 

9

215

0.048

0.983

88.9

  1. Comparison made based on the independent subset of Set T (224 siRNA experiments targeting 197 genes). Default settings were used for the 15 online predicting tools. A siRNA experiment was considered effective if it achieved > 70% efficacy (was rated "high" or "very high" efficacy).