|
| Option |
-% percent_of_sequences |
| Default |
-% 100 |
| Description |
This option restricts pattern discovery to patterns
that occur in at least percent_of_sequences% of the total
number of sequences in the InputFile. percent_of_sequences
can be given either as a number between 1 and 100 or as a
fractional number between 0 and 1.
This option is incompatible with -j
|
| Option |
-j min_support |
| Default |
-j 100%_of_sequences_in_InputFile |
| Description |
1) if the option -u is not used, reported patterns
must occur at least min_support times in the InputFile.
2) if the option -u is used, reported patterns must occur in at least
min_support independent sequences in the InputFile.
This option is incompatible with -%
|
| Option |
-k min_tokens_in_window |
| Default |
-k 3 |
| Description |
This is the k0 value in the density
constraint
|
| Option |
-l min_tokens |
| Default |
-l min_tokens_in_window |
| Description |
Reported patterns must have at least min_tokens
tokens |
| Option |
-u |
| Default |
Set |
| Description |
If -u is set, then the min_support option is
interpreted as the minimum number of independent sequences in the InputFile
that must contain the pattern. If -u is not set, the min_support
option is interpreted as the minimum number of times that the
pattern must occur in the InputFile. This option is ignored
if -% is used instead or if neither -% nor -j are used. |
| Option |
-i |
| Default |
not set |
| Description |
Reported patterns must match identically on each
token. This must be used with DNA databases or when a quick
analysis of very large databases is desired. |
| Option |
-b min_identity_tokens |
| Default |
-b 2 |
| Description |
Reported patterns must contain at least min_identiy_tokens
tokens that match exactly. For instance, the pattern [ILMV]..G.S...[DN]
has two tokens matching exactly.
Important: The minimum value of min_identiy_tokens
is 1.
|
|
|
0. SPLASH
1. Algorithm
2. Performance
3. Pattern Discovery
Syntax
DNA/Protein Seq.
Constraints
Statistical Constr.
Similarity Matrix
Parallel Execution
Output Format
Other
4. Exhaustive Discovery
Syntax
5. Hierarchical Discovery
Syntax
6. Search
Syntax
7. References
|
