Table 1. List of the different links available on the NCBI BLAST home page with the default parameters for each link.
| Expect value | Word size | Reward match | Penalty mismatch | Gap existence | Gap extension | Percentage identity | Filtering | Matrix | |
|---|---|---|---|---|---|---|---|---|---|
| Nucleotide | |||||||||
| Discontiguous megaBLAST | 10 | 11 | 1 | −2 | 0 | 2.5 | None | Low complexity; mask for lookup table | – |
| MegaBLAST | 10 | 28 | 1 | −2 | 0 | 2.5 | None | Low complexity | – |
| Standard BLASTN | 10 | 11 | 1 | −3 | 5 | 2 | – | Low complexity | – |
| Short Nucleotide Sequences | 1000 | 7 | 1 | −3 | 5 | 2 | – | None | – |
| Protein | |||||||||
| Standard blastp | 10 | 3 | – | – | 11 | 1 | – | Low complexity | BLOSUM62 |
| Psi-BLAST | 10 | 3 | – | – | 11 | 1 | – | None | BLOSUM62 |
| Phi-BLAST | 10 | 3 | – | – | 11 | 1 | – | None | BLOSUM62 |
| Short Protein Sequences | 20 000 | 2 | – | – | 11 | 1 | – | None | PAM30 |
| RPS-BLAST | 10 | 3 | – | – | 11 | 1 | – | Low complexity | BLOSUM62 |
| Translated | |||||||||
| Blastx | 10 | 3 | – | – | 11 | 1 | – | Low complexity | BLOSUM62 |
| Tblastn | 10 | 3 | – | – | 11 | 1 | – | Low complexity | BLOSUM62 |
| Tblastx | 10 | 3 | – | – | 11 | 1 | – | Low complexity | BLOSUM62 |
| Special Pages | |||||||||
| Genome BLAST pages (blastn) | 0.01 | 28 | 1 | −2 | 0 | 0 | None | Low complexity; Human repeat | – |
An online version of this table (http://www.ncbi.nlm.nih.gov/blast/link_params.html) contains hyperlinks pointing to definitions of the parameters listed.