Table 1.
This table summarizes the outcome of 100 resampling or bootstrapping tests done using the two data sets (prokaryotic lyases and SH2 containing proteins) with different parameter combinations. For each simulation the average adjusted rand index [44] has been calculated. The row marked in italic bold corresponds to the parameters used in the reference protocol. The values marked in bold indicate the changes made compared to the reference protocol.
| Prokaryotic lyases | SH2 containing proteins | ||||||
| Probe length | Pruning threshold | Coverage | Scoring system | Resampling | Bootstrap | Resampling | Bootstrap |
| 25 | 160 | 3 | Blosum62/-12/-1 | 0.959 | 0.991 | 0.844 | 0.854 |
| 50 | 160 | 3 | Blosum62/-12/-1 | 1 | 1 | 0.932 | 0.937 |
| 100 | 160 | 3 | Blosum62/-12/-1 | 0.969 | 0.887 | 0.689 | 0.735 |
| 50 | 40 | 3 | Blosum62/-12/-1 | 0.971 | 0.810 | 0.777 | 0.732 |
| 50 | 80 | 3 | Blosum62/-12/-1 | 1 | 0.982 | 0.753 | 0.803 |
| 50 | 120 | 3 | Blosum62/-12/-1 | 1 | 1 | 0.895 | 0.897 |
| 50 | 160 | 3 | Blosum62/-12/-1 | 1 | 1 | 0.932 | 0.937 |
| 50 | 200 | 3 | Blosum62/-12/-1 | 1 | 1 | 0.948 | 0.935 |
| 50 | 160 | 1 | Blosum62/-12/-1 | 1 | 0.991 | 0.919 | 0.812 |
| 50 | 160 | 2 | Blosum62/-12/-1 | 1 | 0.996 | 0.878 | 0.937 |
| 50 | 160 | 3 | Blosum62/-12/-1 | 1 | 1 | 0.932 | 0.937 |
| 50 | 160 | 3 | Blosum45/-13/-3 | 1 | 0.985 | 0.939 | 0.839 |
| 50 | 160 | 3 | Blosum62/-12/-1 | 1 | 1 | 0.932 | 0.937 |
| 50 | 160 | 3 | Blosum80/-10/-1 | 0.999 | 0.991 | 0.909 | 0.859 |