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Table 2 Performance of pair-wise comparisons for natural candidate CP pairs over various protein sizes

From: CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships

Length of the query protein (residues)

No. of candidate CP pairs

CPSARST

SHEBA

SAMO

  

Structural diversity

Average running time (s)

Structural diversity

Average running time (s)

Structural diversity

Average running time (s)

≤ 100

135

5.269

0.245

6.600

0.506

4.024

0.765

100-150

223

6.629

0.381

10.255

0.767

4.359

2.243

150-200

464

6.105

0.520

12.730

0.955

4.591

3.554

200-250

177

4.410

0.922

10.683

1.390

3.499

6.793

250-300

39

6.645

1.063

11.092

1.774

4.277

10.820

> 300

30

6.918

1.894

6.976

2.224

4.423

22.345

Average

  

0.838

 

1.269

 

7.753

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Genome Biology

ISSN: 1474-760X

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