Table 4.
Homology coverage performance for global and local homologies of different evolutionary models implemented under the e2msa local alignment algorithm
| Homology Coverage | ||||||
|---|---|---|---|---|---|---|
| [AUC for F measure (%)] | ||||||
| Method | Global homology set | Local homology set | ||||
| parameterization | parameterization | |||||
| short | long | optimal | short | long | optimal | |
| e2msa.afg | 74.3 | 86.9 | 86.7 | 69.5 | 73.9 | 78.2 |
| e2msa.aga | 74.4 | 87.3 | 86.5 | 69.6 | 73.1 | 78.0 |
| e2msa.aif | 74.0 | 86.8 | 86.6 | 69.5 | 74.3 | 78.2 |
| e2msa.tkf92 | 74.6 | 86.5 | 86.0 | 69.4 | 73.8 | 77.7 |
| e2msa.afr | 74.6 | 86.4 | 86.0 | 69.3 | 73.6 | 77.5 |
| e2msa.aali | 73.9 | 86.7 | 85.4 | 69.6 | 73.3 | 77.6 |
| e2msa.tkf91 | 72.8 | 79.6 | 78.0 | 67.7 | 72.0 | 72.6 |
| SSEARCH (BLOSUM62, -11/-1) | 86.7 | 77.1 | ||||
| PHMMER (no filters) | 83.3 | 76.7 | ||||
| NCBIBLAST | 85.0 | 72.7 | ||||
| MSAProbs | 99.3 | NA | ||||
| MUSCLE | 99.3 | NA | ||||
In bold, we indicate the best performing of the three alternative parameterizations