Matches and mismatches in nucleotide alignments are scored using identity matrices, which assigned a certain reward (positive score) for matches and a penalty (negative score) for mismatches. They are used to be specified by the NUCL_REWARD (-r, for commandline BLAST) and NUCL_PENALTY (-q for commandline BLAST) parameters in BLAST URLAPI, respectively. The new parameter MATCH_SCORES supersedes them. To ensure accurate evaluation of the alignment significance, only a limited set of combinations are supported. Furthermore, the gap opening and gap extension parameters associated with each reward/penalty combination are restricted. The table below lists the allowed MATCH_SCORES and GAPCOSTS for each supported matrix.
| Table 6.11.1 Nucleotide Matrices and Their Allowed -G/-E Combinations | |
| Nucleotide Matrix | Allowed -G/-E Combinations |
|---|---|
| -r 1 -q -4 | -G 1 -E 2; -G 0 -E 2; -G 2 -E 1; -G 1 -E 1; -G 2 -E 2 |
| -r 1 -q -3 | -G 1 -E 2; -G 0 -E 2; -G 2 -E 1; -G 1 -E 1; -G 2 -E 2 |
| -r 1 -q -2 | -G 1 -E 2; -G 0 -E 2; -G 3 -E 1; -G 2 -E 1; -G 1 -E 1; -G 2 -E 2 |
| -r 1 -q -1 | -G 3 -E 2; -G 2 -E 2; -G 1 -E 2; -G 0 -E 2; -G 4 -E 1; -G 3 -E 1; -G 2 -E1; -G 4 -E 2 |
| -r 2 -q -7 | -G 2 -E 4; -G 0 -E 4; -G 4 -E 2; -G 2 -E 2; -G 4 -E 4 |
| -r 2 -q -5 | -G 2 -E 4; -G 0 -E 4; -G 4 -E 2; -G 2 -E 2; -G 4 -E 4 |
| -r 2 -q -3 | -G 4 -E 4; -G 2 -E 4; -G 0 -E 4; -G 3 -E 3; -G 6 -E 2; -G 5 -E 2; -G 4 -E 2; -G 2 -E 2; -G 6 -E 4 |
| -r 4 -q -5 | -G 6 -E 5; -G 5 -E 5; -G 4 -E 5; -G 3 -E 5; -G 12 -E 8 |
| -r 5 -q -4 | -G 8 -E 6; -G 10 -E 6; -G 25 -E 10 |
Note: Matrix values pair goes to 'MATCH_SCORES', as in '...&MATCH_SCORES=1,-4&...'. Any GAPCOSTS combinations above those in bold will be allowed since ungapped statistics (ungapped threshold) will be applicable. The value pair appears in GAPCOSTS in the order given, as in '...&GAPCOSTS=25+10&...'.