BLAST Search main parameters
- 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.