Table 2.
Experimental results for all competing methods on the remote homology detection task using the mismatch(5,1) kernel.
| neighborhood (no clustering) | clustered neighborhood | |||||
| dataset | ROC | ROC50 | p-value | ROC | ROC50 | p-value |
| PDB | ||||||
| full sequence | .9389 | .7203 | - | .9414 | .7230 | - |
| region | .9698 | .8048 | .0075 | .9705 | .8038 | .0020 |
| no tails (full seq.) | .9379 | .7287 | .9390 | .9378 | .7301 | .7605 |
| max length (full seq.) | .9457 | .7359 | .4725 | .9526 | .7491 | .3817 |
| Swiss-Prot | ||||||
| full sequence | .9253 | .6685 | - | .9378 | .7258 | - |
| region | .9757 | .8280 | .0060 | .9773 | .8414 | .0108 |
| no tails (full seq.) | .9290 | .6750 | .9813 | .9344 | .6874 | .5600 |
| max length (full seq.) | .9185 | .6094 | .1436 | .9223 | .6201 | .0279 |
| NR | ||||||
| full sequence | .9475 | .7233 | - | .9544 | .7510 | - |
| region | .9837 | .8824 | 1.7e-04 | .9874 | .8885 | 1.2e-04 |
| no tails (full seq.) | .9554 | .7083 | .7930 | .9584 | .7211 | .7501 |
| max length (full seq.) | .9508 | .7421 | .7578 | .9518 | .7613 | .9387 |
* p-value: signed-rank test on ROC50 scores against full sequence in the corresponding setting