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 | |