Table 3 Comparison between BLAST, PSIBLAST, FUGUE, DP-FUGUE (Ï„= 3.5, PD, pvalue) and URMS on the training set. The normalized indices (in percentages) are given in parentheses. PSIBLAST's parameters were set to h = 1e-5, e = 100 and j = 10 (although no improvement was observed after the fourth iteration). FUGUE was run using the default parameters.
Index | BLAST | PSIBLAST (2 to 4 iterations) | FUGUE | DP-FUGUE | URMS | ||
|---|---|---|---|---|---|---|---|
| Â | Â | 2 iterations | 3 iterations | 4 iterations | Â | Â | Â |
ROC1-S | 212 (25.64) | 265 (29.80) | 281 (30.91) | 279 (30.68) | 296 (35.03) | 479 (44.63) | 610 (60.20) |
ROC1-F | 212 (21.65) | 265 (24.58) | 281 (25.23) | 279 (25.12) | 306 (28.64) | 594 (36.60) | 719 (51.58) |
TSS | 278 (29.32) | 315 (33.48) | 335 (34.54) | 335 (34.54) | 422 (40.20) | 546 (47.81) | 797 (69.07) |
TFF | 344 (24.76) | 386 (28.08) | 410 (28.84) | 409 (28.81) | 659 (34.72) | 875 (40.64) | 1681 (67.30) |