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Table 2 Increase in the number of true positives or high-quality alignments.

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

Input Evaluation COMER new COMER new (alt.)
   TPs (+%) TPsv1.4 FDR TPs (+%) TPsv1.4 FDR
HHblits MSAs Sensitivity 34902 (7.4) 32483 0.001 33474 (3.1) 32483 0.001
PSI-BLAST MSAs Sensitivity 27666 (34.2) 20612 0.002 26266 (27.4) 20612 0.002
HHblits MSAs Local 75622 (2.9) 73526 0.002 0(0) 0 0
  Global 16699 (15.9) 14414 0.001 18670 (29.5) 14414 0.001
  Local (max ext) 46608 (8.8) 42857 0.005 38090 (10.8) 34367 0.001
  Global (max ext) 43603 (7.6) 40531 0.008 42165 (8.9) 38704 0.006
PSI-BLAST MSAs Local 61222 (4.4) 58627 0.004 13423 (13.4) 11842 0.001
  Global 10248 (43.9) 7123 0.001 11523 (61.8) 7123 0.001
  Local (max ext) 25208 (8.9) 23146 0.004 28819 (24.5) 23146 0.004
  Global (max ext) 25161 (7.3) 23453 0.007 15588 (24.6) 12515 0.003
  1. Shown are the results of the evaluation of the sensitivity and alignment quality (Local and Global evaluation modes) of versions of the COMER method using profiles constructed from HHblits and PSI-BLAST MSAs. TPs stands for the number of true positives (Sensitivity) or high-quality alignments (in the Local and Global evaluation modes) at a specified false discovery rate (FDR) for a new version of the COMER method. TPsv1.4 represents the same number for the previous COMER version. The percentage improvement with respect to TPsv1.4 is given in parentheses. 0 indicates no improvement