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