NCBI BLAST programs support five protein scoring matrices: BLOSUM45, BLOSUM62, BLOSUM80, PAM30, and PAM70. To ensure correct statisitcal evaluation of the found matches, only a limitted number of -G/-E sets. These matrices with their supported -G/-E values are summarized in the table below.
| Table 6.2 Supported -G/-E pairs for protein scoring matrices | |
| Matrix | Allowed -G/-E settings |
|---|---|
| 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 12 -E 2; -G 13 -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 1; -G 10 -E 1; -G 11 -E 1 |
NOTE:
Defaults are in red. To use custom matrix, we have to use old BLAST engine (-V T). Name the custom matrix as one of the supported matrix file and place it in the data directory and call it using -M parameter. The statistics of the alignments identified with custom matrix will NOT be reliable.