Table 3 Comparison in performance between 15 online siRNA design tools and DRM rule sets with four different stringency levels (α = 0.951, 0.895, 0.845 and 0.827).

Ambion siRNA Target Finder

Ambion, Inc.

[64]

190.0

0.603

0.456

37.0%

0.574

0.457

70.3%

Jack Lin's siRNA Sequence Finder

Cold Spring Harbor Laboratory

[65]

207.5

0.204

0.759

30.9%

0.221

0.757

67.1%

siDESIGN Center

Dharmacon, Inc.

[66]

9.8

0.042

0.976

48.5%

0.036

0.982

81.8%

siRNA Target Finder

GenScript Corp.

[67]

22.4

0.032

0.979

44.4%

0.030

0.988

85.2%

Imgenex sirna Designer

Imgenex Corp.

[68]

22.8

0.116

0.913

41.5%

0.108

0.929

77.4%

EMBOSS sirna

Institute Pasteur

[69]

639.4

0.778

0.250

35.4%

0.767

0.258

69.9%

IDT RNAi Design (SciTools)

Integrated DNA Technologies, Inc.

[70]

5.8

0.032

0.975

40.0%

0.030

0.979

76.7%

BLOCK-iT RNAi Designer

Invitrogen Corp.

[71]

11.4

0.026

0.985

47.6%

0.020

0.982

71.4%

siSearch

Karolinska Institutet

[72]

19.6

0.016

0.986

37.5%

0.017

0.991

81.3%

SiMAX

MWG-Biotech, Inc.

[73]

35.1

0.161

0.843

35.3%

0.172

0.872

75.1%

BIOPREDsi

Novartis Institutes for BioMedical Research

[74]

10.0

0.794

0.908

31.3%

0.820

0.899

64.6%

Promega siRNA Target Designer

Promega Corp.

[75]

38.0

0.093

0.941

45.5%

0.083

0.958

81.8%

QIAGEN siRNA Design Tool

QIAGEN, Inc.

[76]

29.6

0.167

0.862

38.9%

0.161

0.881

75.3%

SDS/MPI

University of Hong Kong

[77]

432.8

0.656

0.380

35.9%

0.632

0.368

69.2%

WI siRNA Selection Program

Whitehead Institute

[78]

9.5

0.019

0.992

53.8%

0.015

0.994

84.6%

DRM RS _0.951

18.9

0.021

0.996

72.7%

0.013

0.997

90.9%

DRM RS _0.895

20.7

0.032

0.992

66.7%

0.021

0.994

88.9%

DRM RS _0.845

38.1

0.032

0.986

54.5%

0.026

0.984

90.9%

DRM RS _0.827

51.8

0.037

0.973

42.4%

0.038

0.988

87.9%