Main parameters of BLAST
- Restricts the number of short descriptions of matching
sequences reported to the number specified; default
limit is 100 descriptions. See also EXPECT.
- Restricts database sequences to the number specified for
which high-scoring segment pairs (HSPs) are reported;
the default limit is 100. If more database sequences
than this happen to satisfy the statistical
significance threshold for reporting (see EXPECT below),
only the matches ascribed the greatest statistical
significance are reported.
The statistical significance threshold for reporting
matches against database sequences; the default value
is 10, such that 10 matches are expected to be found
merely by chance, according to the stochastic model
of Karlin and Altschul (1990). If the statistical
significance ascribed to a match is greater than the
EXPECT threshold, the match will not be reported.
Lower EXPECT thresholds are more stringent, leading
to fewer chance matches being reported. Fractional
values are acceptable.
- FILTER (Low-complexity)
Mask off segments of the query sequence that have
low compositional complexity, as determined by the
SEG program of Wootton & Federhen (Computers and
Chemistry, 1993) or, for BLASTN, by the DUST
program of Tatusov and Lipman (in preparation).
Filtering can eliminate statistically significant but
biologically uninteresting reports from the blast
output (e.g., hits against common acidic-, basic- or
proline-rich regions), leaving the more biologically
interesting regions of the query sequence available
for specific matching against database sequences.
Filtering is only applied to the query sequence (or
its translation products), not to database sequences.
Default filtering is DUST for BLASTN, SEG for other
It is not unusual for nothing at all to be masked
by SEG, when applied to sequences in SWISS-PROT,
so filtering should not be expected to
always yield an effect. Furthermore, in some cases,
sequences are masked in their entirety, indicating that
the statistical significance of any matches reported
against the unfiltered query sequence should be suspect.
- FILTER (Mask for lookup table only)
This option masks only for purposes of constructing the lookup
table used by BLAST. The BLAST extensions are performed without
masking. This option is still experimental and may change in the
- Reward and Penalty for Nucleotide Programs
Many nucleotide searches use a simple scoring system that consists of a "reward" for a match and a "penalty" for a mismatch. The (absolute) reward/penalty ratio should be increased as one looks at more divergent sequences. A ratio of 0.33 (1/-3) is appropriate for sequences that are about 99% conserved; a ratio of 0.5 (1/-2) is best for sequences that are 95% conserved; a ratio of about one (1/-1) is best for sequences that are 75% conserved .
To ensure BLAST returns more reliable statistics for blastn searches, NCBI has put new restraint on the allowed reward/penalty pairs and their associated gap existence and gap extension penalties. See News on blast 2.2.13 for more information.
 States DJ, Gish W, and Altschul SF (1991) METHODS: A companion to Methods in Enzymology 3:66-70.
- Graphical Overview
An overview of the database sequences aligned to the query
sequence is shown. The score of each alignment is indicated
by one of five different colors, which divides the range
of scores into five groups. Multiple alignments on the
same database sequence are connected by a striped line.
Mousing over a hit sequence
causes the definition and score to be shown in the
window at the top, clicking on a hit sequence takes the user to
the associated alignments.