Accept criteria determine whether an alignment is a hit, also
called an accept. See also weak hits.
Hits are written to the output
files. In clustering commands (cluster_fast and cluster_smallmem), accept options
determine whether or not a sequence matches a cluster centroid and
should be assigned to that cluster.
For global searches and clustering, the
‑id option must be specified. For local searches, the ‑evalue
option must be specified and -id is optional. Other accept criteria
are always optional.
Accept criteria do not have default
values.
If more than one accept option is
specified, they are combined with AND, so all of them must be
satisfied.
Criteria that do not require an alignment,
e.g. ‑idprefix and ‑minqt, are tested before an alignment is
computed; these can give significant improvements in speed because
a target can be rejected without the overhead of computing an
alignment. Most of these are not supported by local search commands
(ublast, usearch_local and
search_local).
| Option |
Real/
Integer |
Global/
Local |
Need aln? |
Description |
|
‑evalue |
r |
L |
Y |
Maximum E-value.
Required for most commands that use local alignments. |
|
‑id |
r |
GL |
Y |
Minimum identity. Required for most commands that
use global alignments. |
|
‑query_cov |
r |
GL |
Y |
Fraction of the query sequence that is
aligned, in the range 0.0 to 1.0. |
|
‑target_cov |
r |
GL |
Y |
Fraction of the target sequence that is
aligned, in the range 0.0 to 1.0. |
|
‑idprefix |
N |
G |
N |
First N letters are identical. |
|
‑idsuffix |
N |
G |
N |
Last N letters are identical. |
|
‑minqt |
r |
G |
N |
Minimum value of query_seq_length /
target_seq_length. |
|
‑maxqt |
r |
G |
N |
Maximum value of query_seq_length /
target_seq_length. |
|
‑minsl |
r |
G |
N |
Minimum value of shorter_seq_length /
longer_seq_length. |
|
‑maxsl |
r |
G |
N |
Maximum value of shorter_seq_length /
longer_seq_length. |
|
‑leftjust |
|
G |
Y |
No terminal gaps at start of
alignment. |
|
‑rightjust |
|
G |
Y |
No terminal gaps at end of
alignment. |
|
‑self |
|
GL |
N |
Reject if labels are identical (i.e., reject self-hits).
Requires v.6.0.280 or later. |
|
‑selfid |
|
G |
N |
Reject if sequences are identical (i.e., don't want
self-hits). Requires v.6.0.280 or later. |
|
‑maxid |
r |
GL |
Y |
Reject if identity is greater. Example: to select hits
that are 97% identical to two significant figures use ‑id 0.965 ‑maxid
0.975. Requires v6.0.284 or later. |
|