Alignment heuristic parameters control fast but approximate methods
for finding the alignment with the highest score. These are
distinct from alignment scoring
parameters, which determine the score of an alignment. Ideally,
changing heuristic parameters would not change the reported
alignment (because the best alignment would always be found). By
contrast, changing alignment scoring parameters will tend to change
the alignment, e.g. increasing gap penalties will reduce the number
of gaps.
Full dynamic programming
Heuristics can be disabled entirely by using the ‑fulldp option,
which specifies that full dynamic programming algorithms should be
used. These algorithms (Needleman-Wunsch
for global alignments and Smith-Waterman
for local alignments) are much slower than the heuristic algorithms
that USEARCH uses by default, but guarantee to find alignments with
the maximum possible score.
Local alignment
heuristics
| Option |
Default |
Description |
|
‑xdrop_u |
16.0 |
X-drop for ungapped extension. |
|
‑xdrop_g |
32.0 |
X-drop for gapped extension. |
|
‑hspw |
5 nt, 3 aa |
Word length for seeding HSPs (ignored by
ublast). |
Global alignment
heuristics
| Option |
Default |
Description |
|
‑xdrop_nw |
16.0 |
X-drop for HSP-finding. |
|
‑minhsp |
32 |
Minimum HSP length. This sets an upper limit on the
minimum [sic]; USEARCH will automatically reduce this limit for
short sequences as needed. |
|
‑band |
16 |
Minimum band radius for filling gaps between
HSPs. The width of the band is 2 x radius + 1, so default width is 33. Smaller
values improve speed. Longer values produce better alignments when there are
many non-terminal gaps, especially long gaps, in one sequence relative to the
other. |
|
‑hspw |
5 nt, 3 aa |
Word length for seeding HSPs. |
|