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Table 1 Area under the ROC curve and improvement of the COMER method

From: Estimating statistical significance of local protein profile-profile alignments

Input

Evaluation

x

COMER new

COMER new (alt.)

COMER v1.4

   

ROCx

Z (p-value)

ROCx

Z (p-value)

ROCx

HHblits MSAs

Sensitivity

6000

0.837

0.9 (0.350)

0.836

0.6 (0.571)

0.835

PSI-BLAST MSAs

Sensitivity

6000

0.705

5.6 (1.7×10−8)

0.698

2.6 (0.009)

0.690

HHblits MSAs

Local

150

0.782

0.9 (0.350)

0.753

−0.9 (0.352)

0.768

 

Global

10000

0.456

8.6 (<3×10−16)

0.456

7.3 (3.8×10−13)

0.438

 

Local (max ext)

1000

0.628

9.0 (<3×10−16)

0.624

7.1 (1.7×10−12)

0.591

 

Global (max ext)

1700

0.603

7.6 (3.9×10−14)

0.598

7.2 (7.7×10−13)

0.574

PSI-BLAST MSAs

Local

400

0.642

1.6 (0.103)

0.623

0.2 (0.874)

0.621

 

Global

22000

0.330

3.7 (2.2×10−4)

0.334

4.9 (1.2×10−6)

0.321

 

Local (max ext)

2500

0.496

5.3 (1.2×10−7)

0.499

6.3 (2.8×10−10)

0.477

 

Global (max ext)

5000

0.471

5.1 (3.0×10−7)

0.474

5.6 (2.1×10−8)

0.457

  1. The sensitivity and alignment quality (Local and Global evaluation modes) of versions of the COMER method are evaluated. Maximally extended (max ext) COMER alignments are included in the evaluation. Profiles were constructed from HHblits and PSI-BLAST MSAs. ROCx is the ROC score calculated up to x false positives (FPs; Sensitivity) or low-quality alignments (LQAs; alignment quality in the Local and Global modes). The number of FPs or LQAs, x, depends on the evaluation mode (see also Fig. 5). Z is the difference between the areas (ROCx scores) obtained for a new and the previous (v1.4) versions of the COMER method, divided by the estimated standard error. The statistical significance of Z is indicated in parentheses