Tabel 2.
Training Set Optimized to Find a Better Sequence Selection Using the rvET, ivET, and Shannon Entropy Methods for the Individual Quality Measures
| 〈zo〉 | |||
|---|---|---|---|
| Q | rvET | ivET | Shannon Entropy |
| No pruning | 3.14 | 1.08 | 3.28 |
| Pruning only | 3.71 | 2.98 | 3.61 |
| Cluster, 1 | 3.75 (+1.1%) | 3.39 (+13.8%) | 3.65 (+1.1%) |
| Cluster, 2 | 3.89 (+4.9%) | 3.38 (+13.4%) | 3.69 (+2.2%) |
| Cluster, 3 | 4.06 (+9.4%) | 3.45 (+15.8%) | 3.70 (+2.5%) |
| Surface | 4.05 (+9.2%) | 3.45 (+15.8%) | 3.64 (+0.8%) |
| Sequence | 3.96 (+6.7%) | 3.35 (+12.4%) | 3.76 (+4.2%) |
| Contrast | 4.07 (+9.7%) | 3.45 (+15.8%) | 3.71 (+2.8%) |
| RI | 3.68 (−0.8%) | 3.08 (+3.4%) | 3.58 (−0.8%) |
| Combined measure | 4.16 (+12.1%) | — | — |
All quality measures were shown to improve the overlap except the QRI which decreased the overlap measure 〈zo〉 in the case of the rvET and Shannon Entropy methods. The small decrease of 〈zo〉 due to QRI optimized may be because the value of the measure is already near maximized. The optimization with the ivET method had a larger improvement due to a new sequence selection but did not give the equivalent results of the rvET method before optimization. The 〈zo〉 for the pruned set is considered the original/starting value for the alignments described in “Materials and Methods” section.