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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