Matches and mismatches in protein alignments are scored using different scoring matrices, which assigned a certain reward for matches and a penalty for mismatches. Only five matrices are currently supported by BLAST. Further more, the number of gap opening and gap extension parameters associated with each matrix is restricted to ensure the accurate evalutation of alignment significance. The table below lists the allowed 'GAPCOSTS' for each matrix.
| Table 6.11.2 Protein Matrices and Their Allowed -G/-E Combinations | |
| Protein Matrix | Allowed -G/-E Combinations |
|---|---|
| PAM30 | -G 5 -E 2; -G 6 -E 2; -G 7 -E 2; -G 8 -E 1; -G 9 -E 1; -G 10 -E 1 |
| PAM70 | -G 6 -E 2; -G 7 -E 2; -G 8 -E 2; -G 9 -E 2; -G 10 -E 1;-G 11 -E 1 |
| BLOSUM45 | -G 10 -E 3; -G 11 -E 3; -G 12 -E 3; -G 13 -E 3; -G 12 -E 2; -G 13 -E 2; -G 14 -E 2; -G 14 -E 2; -G 15 -E 2; -G 16 -E 2; -G 15 -E 1; -G 16 -E 1; -G 17 -E 1; -G 18 -E 1; -G 19 -E 1 |
| BLOSUM62 | -G 7 -E 2; -G 8 -E 2; -G 9 -E 2; -G 10 -E 1; -G 11 -E 1; -G 12 -E 1 |
| BLOSUM80 | -G 6 -E 2; -G 7 -E 2; -G 8 -E 2; -G 9 -E 2; -G 10 -E 1; -G 11 -E 1 |