Table III.
Methods Comparison
| TP not found by |
|||||||||
|---|---|---|---|---|---|---|---|---|---|
| Recall (%) | Precision (%) | TP | FP | FN | Unknown specificity | BLASTP | PRATT | ||
| Scan2S-GATC | 13 | 100 | 14 | 0 | 97 | 2 | 10 | 12 | |
| BLASTP-GATC | 9 | 100 | 9 | 0 | 102 | 0 | 0 | 6 | |
| PRATT-GATC | 3 | 100 | 3 | 0 | 108 | 0 | 0 | 0 | |
| MAGIIC-PRO | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | |
| PSI-BLAST (MPI) | 5 | 100 | 5 | 0 | 106 | 0 | 0 | 2 | |
| HHPred versus pfamA | 2 | 100 | 2 | 0 | 109 | 0 | 0 | 0 | |
| Scan2S-CCGG | 31 | 88 | 14 | 2 | 31 | 1 | 6 | 10 | |
| BLASTP-CCGG | 31 | 93 | 14 | 1 | 31 | 2 | 0 | 8 | |
| PRATT-CCGG | 20 | 100 | 6 | 0 | 24 | 0 | 0 | 0 | |
| MAGIIC-PRO | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | |
| PSI-BLAST (MPI) | 20 | 100 | 8 | 0 | 22 | 0 | 0 | 2 | |
| HHPred versus pfamA | 7 | 100 | 3 | 0 | 42 | 0 | 0 | 0 | |
A comparison of the numbers of true positive (TP), false positive (FP), and false negative (FN) matches found by using Scan2S and alternative methods.