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BLAST options, setting and defaults
BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA databases. BLAST is best used for sequence similarity searching, rather than for motif searching. For searches using a query sequence of fewer than twenty residues, PatMatch is the best choice. Another sequence alignment tool that may yield different results from BLAST, and may be useful for motif searching, is FASTA. To search nonplant datasets, try NCGR BLAST or NCBI BLAST.
A fairly complete on-line guide to BLAST searching can be found at the NCBI BLAST Help Manual. For a theoretical overview of BLAST, see the NCBI BLAST Course. Additional information can be found in the BLAST 2.0 Release Notes
| BLASTN | BLASTP | BLASTX | TBLASTN | TBLASTX | PSIBLAST | |
|---|---|---|---|---|---|---|
| Gap opening penalty: cost to open a gap [integer] |
default = 5 | default = 11 limited values are supported |
default = 11 limited values are supported |
default = 11 limited values are supported |
default = 11 limited values are supported |
default = 5 |
| Gap extension penalty: cost to extend a gap [integer] |
default = 2 | default = 1 a 0 in this field means to use the default |
default = 1 a 0 in this field means to use the default |
default = 1 a 0 in this field means to use the default |
default = 1 a 0 in this field means to use the default |
default = 2 |
| Nucleic match: reward for a match in the BLAST portion of run [integer] |
default = 1 | n/a | n/a | n/a | n/a | default = 1 |
| Nucleic mismatch: penalty for a mismatch in the blast portion of run [integer] |
default = -3 | n/a | n/a | n/a | n/a | default = -3 |
| Expectation value: (E) [real] |
default = 10.0 | default = 10.0 | default = 10.0 | default = 10.0 | default = 10.0 | default = 10.0 |
| Word size: the size of the initial word that must be matched between the database and the query sequence |
default = 11 | default = 3 | default = 3 | default = 3 | default = 3 | default = 11 |
| Max scores: Number of one-line descriptions (V) [Integer] |
default = 25 | default = 25 | default = 25 | default = 25 | default = 25 | default = 25 |
| Max alignments: number of alignments to show (B) [integer] |
default = 15 | default = 15 | default = 15 | default = 15 | default = 15 | default = 15 |
| Query filter: filter applied to the query sequence |
default = DUST | default = SEG | default = SEG | default = SEG | default = SEG | default = DUST |
| Query genetic code: genetic code to be used in BLASTX translation of the query |
n/a | n/a | default = universal | default = universal | default = universal | n/a |
| Matrix: substitution matrix to be used for amino acid comparisons |
no default | default = blosum62 | default = blosum62 | default = blosum62 | default = blosum62 | no default |
Supported and Suggested Values for Gap Open and Extension in BLASTP, BLASTX, TBLASTN, and TBLASTX
| Gaps Open | Gap Extension |
|---|---|
| 10 | 1 |
| 10 | 2 |
| 11 | 1 |
| 8 | 2 |
| 9 | 2 |
