Nucleotide blast searches through megablast, blastall, and bl2seq have until now allowed users to select arbitrary gap existence and gap extension penalties for a blastn type search. This has been convenient for users but has led to the unfortunate situation that searches with some parameter sets were significantly overestimating the statistical significance of matches. The parameters that might cause an issue here are -r, -q, -G, and -E.
To address this, the proper statistical parameters for a number of -r/-q/-G/-E values have been calculated starting from version 2.2.13. Note that above a certain gap existence and extension penalty any value is permitted, as the statistics for un-gapped searches can be used. These are marked as "un-gapped threshold" below.
| Table 6.1 Supported Nucleotide Score Matrices and Their Allowed -G/-E Inputs | |
| Matrix | Allowed -G/-E settings |
|---|---|
| -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 -E 1; -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:
Values in red are threshold for un-gapped statistics. Any value higher than them will be supported. Set marked by * is not supported by megablast.