Table 3.
FN distance (× 10) for putative orthologs data set. Average FN distance (multiplied by 10) for each reference set of the putative orthologs data set. For word-based methods, we show the best performing word length k for each alphabet A. Methods are ordered according to their rank sums ∑R.
| Reference set | ||||||||
|---|---|---|---|---|---|---|---|---|
|
|
||||||||
| No. |
|
Method |
|
k | F-S | F-L | M-S | M-L |
| 1 | 15.5 | d PB-SIM | CE | — | 0.607 | 0.272 | 0.735 | 0.866 |
| 2 | 16.5 | d PB-ML | CE | — | 0.536 | 0.272 | 0.837 | 0.984 |
| 3 | 18.0 | d S | AA | 3 | 0.473 | 0.167 | 0.937 | 1.252 |
| 4 | 22.0 | d F | AA | 4 | 0.580 | 0.304 | 0.840 | 1.042 |
| 5 | 23.5 | d PB-ML | AA | — | 0.533 | 0.272 | 0.754 | 1.337 |
| 6 | 27.5 | d PB-SIM | AA | — | 0.650 | 0.385 | 0.712 | 1.053 |
| 7.5 | 37.0 | d P | AA | 4 | 0.713 | 0.353 | 0.880 | 1.182 |
| 7.5 | 37.0 | d F | CE | 6 | 0.657 | 0.256 | 1.022 | 1.337 |
| 9 | 38.5 | d S | CE | 4 | 0.533 | 0.272 | 1.338 | 1.393 |
| 10 | 44.0 | d LZ | AA | — | 0.763 | 0.423 | 0.897 | 1.074 |
| 11 | 45.5 | B-bin | AA | 3 | 0.747 | 0.337 | 0.869 | 1.402 |
| 12.5 | 47.0 | d E | AA | 4 | 0.697 | 0.449 | 0.998 | 1.259 |
| 12.5 | 47.0 | d P | CE | 4 | 0.833 | 0.176 | 1.170 | 1.344 |
| 14 | 49.0 | d E | CE | 6 | 0.800 | 0.353 | 0.991 | 1.328 |
| 15 | 49.5 | d LZ | CE | — | 0.673 | 0.337 | 1.004 | 1.465 |
| 16 | 53.0 | B-bin | CE | 4 | 0.840 | 0.224 | 1.139 | 1.619 |
| 17 | 55.5 | d ACS | AA | — | 0.713 | 0.385 | 1.454 | 1.305 |
| 18 | 64.0 | d ACS | CE | — | 0.973 | 0.321 | 1.453 | 1.437 |
| 19.5 | 75.0 | d C | AA | 4 | 0.847 | 0.978 | 1.413 | 2.374 |
| 19.5 | 75.0 | d C | CE | 4 | 0.807 | 1.346 | 1.832 | 2.183 |