Below are listed the default parameter values for the CGD implementation of NCBI BLAST+. For a complete description of BLAST programs and parameters, please see NCBI's BLAST Help Page.
| Program | Task | Low Complexity Filter | Expect Threshold | Gapped Alignments | Gap Creation Penalty | Gap Extension Penalty | Nucleotide Match Score | Nucleotide Mismatch Score | Amino Acid Substitution Matrix | Word Length | Word Neighborhood Threshold | Multiple-hits Window Size |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| blastn | megablast | DUST | 10 | Yes | 0 | 0 | 1 | -2 | NA | 28 | NA | 0 (one-hit) |
| blastn | dc-megablast | DUST | 10 | Yes | 5 | 2 | 2 | -3 | NA | 11 | NA | 40 |
| blastn | blastn | DUST | 10 | Yes | 5 | 2 | 2 | -3 | NA | 11 | NA | 0 (one-hit) |
| blastn | blastn-short | DUST | 10 | Yes | 5 | 2 | 1 | -3 | NA | 7 | NA | 0 (one-hit) |
| blastp | blastp | none | 10 | Yes | 11 | 1 | NA | NA | BLOSUM62 | 3 | 11 | 40 |
| blastp | blastp-short | none | 10 | Yes | 9 | 1 | NA | NA | PAM30 | 2 | 16 | 15 |
| blastx | NA | SEG | 10 | Yes | 11 | 1 | NA | NA | BLOSUM62 | 3 | 12 | 40 |
| tblastn | NA | SEG | 10 | Yes | 11 | 1 | NA | NA | BLOSUM62 | 3 | 13 | 40 |
| btlastx | NA | SEG | 10 | NA | NA | NA | NA | NA | BLOSUM62 | 3 | 13 | 40 |