Table 2 The matrix test sets assessed in the homology search performance evaluation
From: PFASUM: a substitution matrix from Pfam structural alignments
Test set | Algorithm | Matrix numbers |
|---|---|---|
PFASUM Search Matrices | PFASUM | [11,100] |
Standard Search Matrices | BLOSUM | 50,62,80 |
| Â | MD | 10,20,40 |
| Â | Optima | 5 |
| Â | PAM | 120,250 |
| Â | VTML | 10,20,40,80,120,160,200 |