Table 2.
Test on PREFAB database
| Method | Set 1 (0.121/420) | Set 2 (0.185/421) | Set 3 (0.248/420) | Set 4 (0.527/421) | All (0.270/1682) |
|---|---|---|---|---|---|
| PROMALS3D (D + S) | 0.817 | 0.879 | 0.921 | 0.954 | 0.893 |
| PROMALS3D (F + S) | 0.745 | 0.850 | 0.896 | 0.947 | 0.859 |
| PROMALS3D (T + S) | 0.766 | 0.856 | 0.902 | 0.950 | 0.869 |
| PROMALS3D (D + F + S) | 0.818 | 0.886 | 0.919 | 0.952 | 0.894 |
| PROMALS3D (D + T + S) | 0.834 | 0.884 | 0.922 | 0.953 | 0.898 |
| PROMALS3D (F + T + S) | 0.794 | 0.875 | 0.909 | 0.952 | 0.883 |
| PROMALS3D (D + F + T + S) | 0.836 | 0.894 | 0.917 | 0.956 | 0.900 |
| PROMALS | 0.570 | 0.771 | 0.875 | 0.946 | 0.790 |
| SPEM | 0.536 | 0.756 | 0.865 | 0.940 | 0.774 |
| MUMMALS | 0.457 | 0.693 | 0.834 | 0.939 | 0.731 |
| ProbCons | 0.428 | 0.672 | 0.826 | 0.936 | 0.716 |
| MAFFT-linsi | 0.443 | 0.681 | 0.826 | 0.938 | 0.722 |
| MUSCLE | 0.372 | 0.631 | 0.787 | 0.930 | 0.680 |
| ClustalW | 0.299 | 0.536 | 0.726 | 0.906 | 0.617 |
The first seven methods (PROMALS3D) for MSAs use both sequence and 3D structural information. The other methods construct multiple alignments using only sequence information (PROMALS and SPEM also use predicted secondary structures). For the meaning of the letters inside the parenthesis after the method names, refer to Table 1. Average Q-score (see Table 1 for definition) is reported. The total 1682 PREFAB alignments are divided to four semi-equal-sized sets according to sequence identity of the reference alignment. The average sequence identity and the number of alignments are in parentheses beneath the set names. The best scores are in bold letters.